After two seasons in the Ontario Provincial Junior A Hockey League (OPJHL) with the Wexford Raiders, Winnik joined the college hockey ranks with the University of New Hampshire of Hockey East. Following his freshman year, Winnik was drafted 265th overall in the 2004 NHL Entry Draft by the Phoenix Coyotes. He found his scoring touch with the Wildcats in his sophomore year scoring 18 goals for 40 points and was one of UNH's best in being named in the NCAA Northeast Regional All-Tournament team. In his junior year Daniel consolidated his break out year by leading the Wildcats with 26 assists and finishing 5th in the Hockey East in scoring with 41 points. He was named as Hockey East player of the month for November and was selected to the Hockey East Second All-Star Team. After completing a three-year career with New Hampshire he signed a three-year entry level contract with the Coyotes on March 31, 2006. He immediately made his professional debut with AHL affiliate, the San Antonio Rampage, to finish the 2005–06 season.

In his first full professional year in 2006–07, Winnik played in a checking role with the Rampage scoring 21 points in 66 games while also spending a stint in the ECHL with secondary affiliate, the Phoenix RoadRunners. In 2007–08, Winnik made the Coyotes line-up out of training camp and scored his first NHL goal in his debut on October 4, 2007 in a 3–2 win against the St. Louis Blues. At the end of his first NHL year Winnik had established himself as a regular in the Coyotes team and was looked upon, by coach Wayne Gretzky, as the team's top penalty killer.

After a promising start to his NHL career, Dan suffered a sophomore slump in 2008–09, scoring just 7 points in 49 games. Seldom used as a reserve forward he was assigned to San Antonio on a 5-game conditioning stint on January 1, 2009. He was then re-signed to an arbitrated one-year contract on July 24, 2009. Winnik quickly rebounded in the following 2009–10 season, regaining a checking line role and finding his scoring touch, tying his career high with 15 assists. As part of a resurgent Coyotes team he made his playoff debut appearing scoreless in 7 games against the Detroit Red Wings.

On June 28, 2010, Winnik was traded by the Coyotes to the Colorado Avalanche for a fourth round pick in the 2012 NHL Entry Draft. He was then signed to a two-year contract with the Avalanche on July 2, 2010.

Unable to agree to terms with the Sharks on a new contract, Winnik was signed as a free agent to a two-year deal with Division rivals, the Anaheim Ducks on July 20, 2012.

On July 28, 2014, Winnik signed as a free agent to a one-year contract with his hometown team, the Toronto Maple Leafs, worth $1.3 million. In the 2014–15 season, Winnik proved a versatile asset for the Maple Leafs with his penalty killing abilities and scoring touch, notching 25 points in 58 appearances, and having spent time on all four lines. On February 25, 2015, with the Maple Leafs out of playoff contention, he was traded to the Pittsburgh Penguins in exchange for Zach Sill, a 2015 fourth round pick and a 2016 second round pick. In 21 games with the Penguins, Winnik collected 2 goals and 9 points but was unable to help the Penguins to a deep playoff run.

On July 1, 2015, Winnik, by this time a fan favourite in Toronto, returned to the Maple Leafs, signing as a free agent on a two-year deal. Winnik's offensive production declined from his previous season with the Maple Leafs, though he remained a concrete part of the penalty kill. On February 28, 2016, the eve of the trade deadline, Winnik was traded to the Washington Capitals, along with a 5th round selection (Beck Malenstyn) in the 2016 draft, in exchange for forward Brooks Laich, prospect defenceman Connor Carrick and a 2nd round draft pick in 2016 (Carl Grundström).

After collecting a career best 12 goals and contributing with 25 points in 72 games for the Presidents' Trophy winning Capitals in the 2016–17 season, Winnik became a free agent at the conclusion of his contract.

Surprisingly going un-signed over the summer, Winnik accepted an invitation to attend the Minnesota Wild's 2017 training camp on a professional try-out contract. On the opening day of the 2017–18 season, Winnik secured a one-year deal with the Wild on October 4, 2017.