Whitman was born on June 24, 1941, in Lake Worth, Florida, the eldest of three sons born to Margaret E. (Hodges) (1922–1966) and Charles Adolphus "C. A." Whitman Jr. (1919–2001). Whitman's father was raised in an orphanage in Savannah, Georgia, and described himself as a self-made man. In 1940, he married Margaret, then 17 years old. The marriage of Whitman's parents was marred by domestic violence; Whitman's father was an admitted authoritarian who provided for his family but demanded near perfection from all of them. He was known to physically and emotionally abuse his wife and children.

On September 1, 1955, Whitman entered St. Ann's High School in West Palm Beach, where he was regarded as a moderately popular student whose intelligence was noted by his teachers and peers. By the next month, he had saved enough money from his newspaper route to purchase a Harley-Davidson motorcycle, which he used on his route.

During Whitman's initial 18-month Service in 1959 and 1960, he earned a sharpshooter's badge and the Marine Corps Expeditionary Medal. He achieved 215 of 250 possible points on marksmanship tests, doing well when shooting rapidly over long distances as well as at moving targets. After completing his assignment, Whitman applied to a U.S. Navy and Marine Corps scholarship program, intending to complete college and become a commissioned officer.

On September 15, 1961, Whitman entered the mechanical engineering program at the University of Texas at Austin. He was initially a poor student. His hobbies included karate, scuba diving, gambling, and hunting. Shortly after his enrollment at the university, Whitman and two friends were observed poaching a deer, with a passer-by noting his license plate number and reporting them to the police. The trio were butchering the deer in the shower at Whitman's dormitory when they were arrested. Whitman was fined $100 ($800 in 2017) for the offense.

On August 17, 1962, Whitman and Leissner were married in a Catholic ceremony held in Leissner's hometown of Needville, Texas. The couple chose the 22nd wedding anniversary of Whitman's parents as the date for their wedding. Whitman's family drove from Florida to Texas to attend the event, and his younger brother Patrick served as best man. Fr. Leduc, a Whitman family friend, presided over the ceremony. Leissner's family and friends approved of her choice of husband, describing Whitman as a "handsome young man" who was both intelligent, and aspirational.

While awaiting his court martial in 1963, Whitman began to write a diary titled "Daily Record of C. J. Whitman." In it, he wrote about his daily life in the Marine Corps and his interactions with Kathy and other family members. He also wrote about his upcoming court martial and contempt for the Marine Corps, criticizing them for inefficiencies. In his writings about his wife, Whitman often praised her and expressed his longing to be with her. He also wrote about his efforts and plans to free himself from financial dependence on his father.

In December 1964, Whitman was honorably discharged from the marines. He returned to the University of Texas at Austin, enrolling in the architectural engineering program. To support Kathy and himself, he worked as a bill collector for the Standard Finance Company. Later, he worked as a bank Teller at the Austin National Bank. In January 1965, Whitman took a temporary job with Central Freight Lines as a traffic surveyor for the Texas Highway Department. He also volunteered as a scout leader for Austin Scout Troop 5, while his wife Kathy now worked as a biology Teacher at Lanier High School.

Investigating officers found that Whitman had visited several University doctors in the year before the shootings; they prescribed various medications for him. Whitman had seen a minimum of five doctors between the fall and winter of 1965, before he visited a Psychiatrist from whom he received no prescription. At some other time he was prescribed Valium by Dr. Jan Cochrum, who recommended he visit the campus Psychiatrist.

A joint Catholic funeral Service for Whitman and his mother was held in Lake Worth, Florida, on August 5, 1966. They were buried in Florida's Hillcrest Memorial Park. Since he was a military veteran, Whitman was buried with military honors; his casket was draped with the American flag.

At approximately 11:35 a.m., Whitman arrived on the University of Texas at Austin campus. He falsely identified himself as a research assistant and told a security guard he was there to deliver equipment. He then climbed to the 28th floor of the UT tower and opened fire from the observation deck with a hunting rifle and other weapons.

As a boy, Whitman was described as a polite child who seldom lost his temper. He was extremely intelligent—an examination at the age of six revealed his IQ to be 139. Whitman's academic achievements were encouraged by his parents, yet any indication of failure or a lethargic attitude were met with discipline—often physical—from his father.

In Austin, Whitman's mother took a job in a cafeteria and moved into her own apartment, though she remained in close contact with Charles. Whitman's father later said he had spent more than a thousand dollars ($8,000 in 2017) on long-distance phone calls to both his wife and Charles, begging his wife to return and asking his son to convince her to come back. During this stressful time, Whitman was abusing amphetamines and began experiencing severe headaches, which he described as being "tremendous."