McNamara's managerial tactics during the 1986 World Series (especially in the last two games) received much criticism and scrutiny. In the pivotal sixth game, McNamara removed Red Sox ace Roger Clemens in the eighth inning despite the fact that Clemens was still pitching well. Both parties have different stories regarding Clemens's departure. According to Clemens, he did not want to leave the game, but McNamara insisted that Clemens asked to be taken out because he had a blister on his pitching hand. McNamara was also criticized for pinch-hitting Clemens with rookie Mike Greenwell, who struck out on three pitches, when veteran slugger Don Baylor was also available. McNamara's move was further questioned in light of the relatively poor performances of closer Calvin Schiraldi and longtime reliever Bob Stanley.
Yet, perhaps the decision that McNamara will be most remembered for is his leaving first baseman Bill Buckner in the game in the 10th inning rather than removing him for a defensive substitute. McNamara was ridiculed for years afterward for leaving Buckner on the field instead of replacing him with Dave Stapleton, who had previously been used to replace Buckner in late innings for defensive purposes (including Games 1 and 5 of the World Series). He later said, "I felt Buckner deserved to be on the field when we won."  The Red Sox players also knew that their manager let sentiment overpower his judgement. Stapleton claimed that "[McNamara] damn well knows that he messed up. And he very well could have cost us the World Series that year." McNamara finally responded to Stapleton's attack in 2011 during an interview with Bob Costas for MLB Network, reneging on his original claim that sentiment was what caused him to keep Buckner in the game and saying that Stapleton had the nickname of "Shaky" because of his poor defense.
With Game 7 delayed a day due to rain in New York, McNamara bumped originally-scheduled starting pitcher Oil Can Boyd in favor of Bruce Hurst. Hurst was asked to pitch on three days' rest and, despite pitching well for five innings, he visibly tired in the sixth, allowing the Mets to score three runs to tie the game. McNamara once again sent Calvin Schiraldi to relieve Hurst, despite Schiraldi's poor performance in Game 6, and despite the fact that Boyd was well-rested and ready to pitch (In a recent interview with the NY Times, McNamara confirms an account of then pitching coach Bill Fischer that Oil Can Boyd was in fact too drunk for relief work in Game 7). Schiraldi gave up a tie-breaking home run to Ray Knight, the first batter he faced, and ended up surrendering three runs while recording only a single out. The Red Sox would lose the game (8-5) and the series (4-3).