On April 20, 2006, with the Nationals' 10–4 victory over the Philadelphia Phillies, Robinson got his 1000th win, becoming the 53rd manager to reach that milestone. He had earned his 1000th loss two seasons earlier.
During a game against the Houston Astros on May 25, 2006, Robinson pulled Nationals catcher Matt LeCroy during the middle of the seventh inning, violating an unwritten rule that managers do not remove position players in the middle of an inning. Instead, managers are supposed to discreetly switch position players in between innings. However, LeCroy, the third-string catcher, had allowed Houston Astros baserunners to steal seven bases over seven innings and had committed two throwing errors. Although the Nationals won the game 8–5, Robinson found the decision so difficult to make on a player he respected so much, he broke down crying during post-game interviews.
On September 30, 2006, the Nationals' management declined to renew Robinson's contract for the 2007 season, though they stated he was welcome to come to spring training in an unspecified role. Robinson, who wanted either a front office job or a consultancy, declined. On October 1, 2006, he managed his final game, a 6–2 loss to the Mets, and prior to the game addressed the fans at RFK Stadium. Robinson's record as a manager stood at 1,065 wins and 1,176 losses.