On January 6, 2003, Timlin signed a one-year, $1.85 million contract with the Boston Red Sox. During the 2003 season, he appeared in 72 games for Boston, compiling a 6–4 record, with 2 saves and a 3.55 ERA. In the postseason, he appeared in three games of the ALDS against the Oakland Athletics, and five games of the ALCS against the New York Yankees. In those eight games, he pitched innings, facing 32 batters while striking out 11 and only giving up two walks, one hit, and no runs. After the season, Timlin was re-signed by the Red Sox to a two-year, $5.25 million contract in November 2003.