Hegan began his major league career with the New York Yankees in 1964, appearing in five games late in the regular season; he was hitless in five at bats. He was added to the Yankees' roster for the 1964 World Series, replacing the injured Tony Kubek. In the series, which the Yankees lost in seven games to the St. Louis Cardinals, Hegan appeared as a substitute in three games; he was hitless in one at bat, with one walk and one run scored. Hegan played 13 games with the Yankees in 1966, batting.205, and 68 games in 1967, batting.136. In June 1968, the Yankees sold his contract to the Seattle Pilots, an expansion team being added to MLB for the 1969 season.
Seattle Pilots
Hegan played 95 games for the Pilots in 1969, batting.292 with eight home runs and 37 RBIs. Hegan hit the first home run in franchise history, in his first at-bat with the team, on April 8. He was selected for the 1969 All-Star Game, but due to an injury was replaced by teammate Don Mincher on the AL roster.
Milwaukee Brewers
After the 1969 season, the Pilots franchise was sold and the team became the Milwaukee Brewers. Hegan played in 148 games for the Brewers during the 1970 season, batting.244 with 11 home runs and 52 RBIs. During the 1970 season, Hegan started an error-less streak as a first basemen, which would last for 178 games – it stood as an American League record until it was broken by Kevin Youkilis on September 7, 2007. Midway through the 1971 season, Hegan was batting.221 when his contract was sold to the Oakland Athletics.
Oakland Athletics
During the second half of the 1971 season, Hegan appeared in 65 games for Oakland, mostly as a pinch hitter or defensive replacement; he batted 13-for-55. In 1972, Hegan appeared in 98 regular season games, batting 26-for-79. In the 1972 World Series, the Athletics defeated the Cincinnati Reds in seven games; Hegan appeared in six games, but was hitless in five at bats. In 1973, Hegan was with Oakland until mid-August, batting 13-for-71 in 75 games played. On August 18, Oakland sent him to the Yankees for future considerations.
New York Yankees (second stint)
Hegan was the Yankees' regular first baseman for the remainder of the 1973 season; appearing in 37 games he hit 36-for-131 with six home runs and 14 RBIs. His father, Jim Hegan, was the Yankees' bullpen coach for manager Ralph Houk at the time. On September 30, 1973, Hegan was the last batter in the original Yankee Stadium before its mid-70s renovation. Hegan was with the Yankees in 1974 through mid-May, appearing in 18 games and batting 12-for-53. On May 13, the Yankees sold his contract to the Brewers.
Milwaukee Brewers (second stint)
During his second stint with the Brewers, Hegan appeared in a total of 297 games, batting.239 with 19 home runs and 88 RBIs. On September 3, 1976, he became the first Brewer to hit for the cycle, in an 11–2 win over the Detroit Tigers. Hegan's major league career ended when he was released by the Brewers on July 15, 1977. In a total of 12 major league seasons, Hegan played in 966 games, batting.242 with 53 home runs and 229 RBIs. Defensively, he recorded a.995 fielding percentage at first base and an overall.993 fielding percentage.
Broadcasting
After his retirement from baseball as a player, Hegan spent the next twelve seasons as a television color commentator for the Brewers. In 1989, he was hired by the Cleveland Indians, and served as a commentator for the team on both radio and television for the next 23 seasons. He retired after the 2011 season, although on May 23, 2012, he filled in as commentator for a game against the Detroit Tigers.