The newly created edition of the Washington Senators franchise picked him up, then traded him to the Kansas City Athletics for pitcher Marty Kutyna on December 29, 1960.

In a three-game span against his former team, the Red Sox, at Municipal Stadium from July 12–14, 1962, Sullivan had seven hits in 11 at bats, with two home runs, although Boston won all three games.

[9] Kansas City had lost 21 of its first 26 games and was lodged in last place in the ten-team American League when McGaha was fired, and they remained in the cellar for the rest of the 1965 season, winning 54 and losing 82 (.397) with Sullivan at the reins.

The American League initially rejected the deal, but reconsidered when Mrs. Yawkey joined the group in May 1978, becoming principal owner, general partner and team president.

Still using the resources of the Yawkey fortune, and benefitting from the depth of the Red Sox farm system that he helped to build, Sullivan acquired players Mike Torrez, Jerry Remy, Dick Drago, Tom Burgmeier and Dennis Eckersley.

Buoyed by the new additions to an already strong team, the Red Sox charged into first place in the 1978 AL East race, but they would squander a 14+1⁄2 game lead over the New York Yankees and then lose a one-game playoff for the division title to miss the postseason completely.

Although manager Don Zimmer is usually cast as the chief culprit for the collapse, Sullivan contributed to the debacle by dealing away useful players such as Bernie Carbo, Ferguson Jenkins, Jim Willoughby and Reggie Cleveland, who were considered to be "clubhouse lawyers."

[12] In December 1980, Sullivan faced the imminent free agency of Rick Burleson, Carlton Fisk and Fred Lynn—Boston's starting shortstop, catcher and center fielder, and the "up the middle" core of the ball club.

The three players, represented by agent Jeremy Kapstein, had been embroiled in a contract dispute with the team in 1976, the first year of free agency, and hard feelings still lingered between them and owners Sullivan and Mrs. Yawkey.

Sullivan was able to trade Burleson for value (young third baseman Carney Lansford and relief pitcher Mark Clear), but then failed to mail contract offers to Lynn and Fisk by MLB's mandated deadline, triggering binding arbitration and unintentionally speeding their free agency.

Sullivan was forced to accept fifty cents on the dollar for Lynn in a trade to the California Angels, who signed him to a multi-year contract, and then lost Fisk outright when the arbitrator declared him a free agent.

During Sullivan's tenure as general manager and chief executive, the Red Sox, with their history as the last pre-expansion MLB team to break the color line, were again criticized for anti-Black bigotry.

In a 1985 public reckoning, the team was sued by former outfielder and coach Tommy Harper for retaliation after the Red Sox fired Harper as a minor league base-running instructor when he shared with the media the club's practice of allowing the all-white Elks Club of Winter Haven, Florida (where the team held spring training) into the Red Sox' Chain of Lakes Park clubhouse to invite white players and white front-office personnel to the Elks' segregated facilities.

[17] Sullivan then retired to the Gulf Coast of Florida, where he operated a marina and invested successfully in real estate, his name occasionally popping up (usually linked with former Commissioner of Baseball Fay Vincent)[18] as a potential part-owner of another Major League club.