Though his record was only 6–6, Flanagan had a 3.33 ERA for the Blue Jays through July 21, 1989. Thereafter, he posted a 5.02 ERA, going 2–4. In 30 games (all starts), he had an 8–10 record, a 3.93 ERA, 47 strikeouts, 47 walks, and 186 hits allowed in innings. Even though he had a losing record, the Blue Jays won the AL East, and Flanagan had his only postseason experience with the Blue Jays. Starting Game 4 in the ALCS against the Athletics, he pitched innings, giving up five runs and three home runs. One of the latter was Jose Canseco's 480-foot (146.30 meters) shot in the third inning, which was the first home run to land in the top deck of the SkyDome. He took the loss in the game, and the Athletics went on to win the series in five games.