Keyes continued his studies at Harvard University, where he resided in Winthrop House, and completed his Bachelor of Arts degree, in government affairs in 1972, graduating magna cum laude. During his first year of graduate school, Keyes's roommate was william Kristol. In 1988, Kristol ran Keyes's unsuccessful U.S. Senate campaign in Maryland.

A year before completing his doctoral studies, Keyes joined the United States Department of State as a protégé of Jeane Kirkpatrick. In 1979, he was assigned to the consulate in Mumbai, India. The following year, Keyes was sent to serve at the embassy in Zimbabwe.

In 1983, President Ronald Reagan appointed Keyes as Ambassador to the United Nations Economic and Social Council. In 1985, he was appointed Assistant Secretary of State for International Organizations, a position he held until 1987. His stay at the UN provoked some controversy, leading Newsday to say "he has propounded the more unpopular aspects of US policy with all the diplomatic subtlety of the cannon burst in Tchaikovsky's 1812 Overture." He also served on the staff of the National Security Council.

Among the U.S. delegation to the 1984 World Population Conference in Mexico City, Keyes was selected by Reagan as deputy chairman. In that capacity, Keyes negotiated the language of the Mexico City Policy to withhold federal funds from international organizations that support abortion. Additionally, Keyes fought against an Arab-backed UN resolution calling for investigation of Israeli settlements. The measure passed, 83–2, with 15 abstentions and only Israel and the U.S. voting against it. Reagan again appointed Keyes to represent the U.S. at the 1985 Women's Conference in Nairobi.

Keyes was appointed Ambassador to the Economic and Social Council of the United Nations by President Ronald Reagan, and served as Reagan's Assistant Secretary of State for International Organization Affairs from 1985 to 1987; in his capacities as a UN ambassador, among Keyes's accomplishments was contributing to the Mexico City Policy.

At a fundraiser for Keyes's senate campaign, President Reagan spoke of Keyes's time as an ambassador, saying that he "did such an extraordinary job ... defending our country against the forces of anti-Americanism." Reagan continued, "I've never known a more stout-hearted defender of a strong America than Alan Keyes." In 1987 Keyes was appointed a resident scholar for the American Enterprise Institute. His principal research for AEI was diplomacy, international relations, and self-government.

In 1988, Keyes was drafted by the Maryland Republican Party to run for the United States Senate, and received 38 percent of the vote against victorious incumbent Democrat Paul Sarbanes.

Following government Service, Ambassador Keyes was President of Citizens Against Government Waste (CAGW) from 1989 to 1991, and founded CAGW's National Taxpayers' Action Day. In 1991, he served as Interim President of Alabama A&M University, in Huntsville, Alabama.

During the 1992 election, Keyes attracted controversy when he took a $8,463/month salary from his campaign fund.

Keyes has worked as a media commentator and talk show personality. In 1994, he began hosting a syndicated radio show called The Alan Keyes Show: America's Wake-Up Call for Radio America from Arlington, Virginia. The show became simulcast on cable's National Empowerment Television in 1997. Keyes also launched various web-based organizations—notably Renew America and the Declaration Foundation, both headquartered in Washington, D.C.

Keyes sought the Republican presidential nomination in 1996, and asked other candidates about abortion in those debates in which he participated. Many Republican Leaders saw this as unnecessary and divisive. Keyes was particularly critical of Clinton during his campaign, saying, "This guy lies, but he lies with passion." He questioned whether a Republican candidate who is truthful, yet cold and heartless, had a chance to win against the incumbent. Keyes was also especially critical of Pat Buchanan, once saying during an interview on the Talk from the Heart program with Al Kresta (simulcast on KJSL St. Louis and WMUZ Detroit) that Buchanan had a "black heart." Keyes's entry into the Republican race after Buchanan had secured victories in New Hampshire and Louisiana led many to believe that Keyes was a stalking horse for neoconservative elements in the Republican Party, since Buchanan had been a well-known ardent foe of abortion and had suffered political fallout for bringing abortion and "cultural war" to the center of the public policy debate. Later during the primaries, Keyes was briefly detained by Atlanta police when he tried to force his way into a debate to which he had been invited, and then uninvited. He was never formally arrested and was eventually picked up 20 minutes later by Atlanta's mayor at the time, Bill Campbell.

Keyes has served on the board of advisors for the Catholic League, a non-profit, Catholic advocacy group headed by william A. Donohue. In 1997, he was quoted as calling in that capacity the ABC television show Nothing Sacred "propaganda dressed up as entertainment, the way the Nazis used to make movies. The entertainment elite's belief that there are no moral absolutes deeply contradicts the religious view of Christianity."

Keyes again campaigned for the Republican nomination in the 2000 primaries on a pro-life, family values, tax reform plank. In Iowa, he finished 3rd, drawing 14 percent in a crowded field. He stayed in the race after the early rounds and debated the two remaining candidates, John McCain and George W. Bush, in a number of nationally televised debates. He finished second in 8 primaries. His best showing in the presidential primaries was in Utah, where he received 20 percent of the vote. He was also noted for jumping into a mosh pit during a Rage Against the Machine song during the Iowa caucus as part of a segment on Michael Moore's TV series The Awful Truth.

In 2002, he hosted a live television commentary show, Alan Keyes Is Making Sense, on the MSNBC cable news channel. The network canceled the show in July, citing poor ratings. The cancellation triggered a currently ongoing boycott led by Jewish education website Mesora.org whose reach numbers more than 72,000 email subscribers. The show was unsympathetic to supporters of the al-Aqsa Intifadah—whom Keyes frequently debated on the program—and supported the Israeli crackdown on Palestinians. The show also featured critical discussion of homosexuality and of Priests accused in the Catholic Church sex abuse scandals. The last episode was broadcast on June 27, 2002. As a result of Keyes's strong advocacy of Israel on his MSNBC show, in July 2002 the state of Israel awarded him a special honor "in appreciation of his journalistic endeavors and his integrity in reporting" and flew him in to meet Prime Minister Ariel Sharon.

In August 2003, Keyes came out in defense of Alabama Chief Justice Roy Moore, citing both the U.S. Constitution and the Alabama constitution as sanctioning Moore's (and Alabama's) authority to publicly display the Ten Commandments in the state's judicial building, in defiance of a court order from U.S. District Judge Myron Thompson. Although the monument was ultimately removed by state authorities, the issue impelled Keyes to spend the next year advocating his understanding of the Constitution's protection of the right of states to display monuments that reflect the religious sentiments of the people in their states. As a result, he published an essay describing his rationale titled "On the establishment of religion: What the Constitution really says."

In November 2006, Keyes criticized Massachusetts governor Mitt Romney for instituting gay marriage entirely on his own—according to Keyes—with no requirement or authority to do so under Massachusetts law. Keyes said Romney's actions, which he suggested were due to a complete misunderstanding of his role as governor and of the limitations of the judicial branch of government, were not necessitated by a ruling of the Massachusetts Supreme Judicial Court in November 2003 that directed the state legislature to institute same-sex marriage. The Massachusetts Supreme Judicial court had ruled that the state law banning same-sex marriage was not constitutional. The court gave the Massachusetts Legislature 180 days to modify the law; after it failed to do so, Romney ordered town clerks to begin issuing marriage licenses on May 17, 2004, in compliance with the court ruling.

In early 2005, Keyes sought to intervene in the Terri Schiavo case, arguing that Schiavo's life was protected by the Florida constitution, and that Governor Jeb Bush had final authority to determine the outcome of the case under state provisions. He attempted to meet with Bush to discuss the provisions of Florida law that authorized the governor to order Schiavo's feeding tubes reinserted—something Bush claimed he wished to do, but for which he said he lacked authority—but the governor declined to meet with Keyes. Keyes subsequently wrote an essay directed openly at Governor Bush titled "Judicial review and executive responsibility", days after Schiavo's feeding tube had been removed.

Keyes also made a widely discussed appearance in the 2006 film Borat. In 2010, About.com, owned by The New York Times Company, named Keyes one of the top 20 conservatives to follow on Twitter.

On December 12, 2007, Keyes participated in the Des Moines Register's Republican presidential debate, televised nationwide by PBS and the cable news networks. This was the first major presidential debate in which Keyes participated during the 2008 election season and the last Republican debate before the Iowa Caucuses. Although Keyes was not listed on the latest national CNN poll leading up to the debate, he registered with at least 1 percent of the Iowa vote in order to participate. During the debate, after the moderator began to ask a question of Texas Congressman Ron Paul, Keyes insisted he was not getting fair treatment. He interrupted the debate moderator at one point, saying that she had not called on him in several rounds and that he had to make an issue of it. He went on the offensive against his opponents during the debate, criticizing Rudy Giuliani's pro-choice position, as well as Mitt Romney's recent change in position on the same subject. In answering a question about global warming, he continued his criticisms of other candidates, saying, "I'm in favor of reducing global warming, because I think the most important emission we need to control is the hot air emission of politicians who pretend one thing and don't deliver". He also advocated ending the income tax, establishing state-sanctioned prayer in public schools, and abolishing abortion. Toward the end of the debate, Keyes stated he could not support Giuliani if he were to win the nomination due to the former New York mayor's position on abortion.

On November 14, 2008, Keyes filed a lawsuit—naming as defendants California Secretary of State Deborah Bowen, President-elect Barack Obama, Vice President-elect Joe Biden, and California's 55 Democratic electors—challenging Obama's eligibility for the U.S. Presidency. The suit requested that Obama provide documentation that he is a natural born citizen of the United States.

In December 2009, Keyes authored a column for the World Net Daily critical of evolution and in support of Intelligent Design.

Keyes was also criticized for his views on homosexuality. In an interview with Michelangelo Signorile, a gay radio host, Keyes defined homosexuality as centering in the pursuit of pleasure, literally "selfish hedonism". When Signorile asked if Mary Cheney, Vice President Dick Cheney's lesbian daughter, fit the description and was therefore a "selfish hedonist", Keyes replied, "Of course she is. That goes by definition." Media sources picked up on the exchange, reporting that Keyes had "trashed", "attacked," and "lashed out at" Mary Cheney, and had called her a "sinner"—provoking condemnation of Keyes by LGBT Republicans and several GOP Leaders. Keyes noted that it was an interviewer, not he, who brought up Mary Cheney's name in the above incident, and he told reporters, "You have tried to personalize the discussion of an issue that I did not personalize. The people asking me the question did so, and if that's inappropriate, blame the media. Do not blame me."

Days after its release, Keyes criticized the 2015 papal encyclical Laudato si', stating that its demands amount to "...global penal colony under the totalitarian control of a government with unprecedented global powers." In the same article Keyes likened the encyclical's author, Pope Francis, to "Marx, Stalin or Mao Zedong."

During the time of the 2016 presidential election, Keyes emerged as a strong critic of Donald Trump. He criticized many conservative Christians for supporting "a candidate whose life could be used to illustrate the deceitfully seductive quality of sin summarized in the phrase 'the glamour of evil.'"

During the campaign, Keyes outlined an alternative to reparations for slavery. His specific suggestion was that, for a period of one or two generations, African-Americans who were descended from slaves would be exempt from the federal income tax (though not from the FICA tax that supports Social Security). Keyes said the experiment "would become a demonstration project for what I believe needs to be done for the whole country, which is to get rid of the income tax." He also called for the repeal of the 17th Amendment in order to require that U.S. Senators be appointed by state legislatures, rather than being directly elected.