Pratt signed with the Mets as a free agent in December of 1996. In the ’97 season, he collected 30 hits for 42 total bases. At Shea Stadium on July 4, Todd had a two-run homer and a run-scoring single in his first game as a Met as the team defeated the Marlins, 6-2. He had three singles and two RBIs in a 4-3 Mets win over the Cubs at Shea on July 17. Pratt had a single and a two-run double in the Mets’ 13-6 victory on August 30 at Baltimore. He also drove in the Mets’ only run in a 2-1 loss to the Phillies in a doubleheader nightcap at Philadelphia on September 15.
In 1998, Pratt had a .275 batting average. In his first game appearance of the season on May 5, he hit a three-run homer in the Mets’ 9-1 win over the Diamondbacks at Shea. Todd hit a three-run triple the next day as the Mets defeated Arizona again, 8-2. At Toronto on July 2, Pratt hit a three-run homer in a 9-1 Mets victory over the Blue Jays. He had a two-run double in a 6-1 Mets triumph over the Brewers in the second game of a doubleheader at Milwaukee on July 22. Todd singled home two runs to start a Mets comeback that led to a 7-6 win over the Giants in 10 innings on August 4 at Shea. He also had an RBI double in an 8-4 Mets victory in a doubleheader nightcap at Houston on September 15.
Todd had 41 hits in 71 games played in 1999. He scored 18 runs and had 21 RBIs during the year. Pratt drove in the winning run with a single in the 11th inning to give the Mets a 4-3 victory over the Expos at Montreal on April 10. He hit a home run in the Mets’ 4-1 win over the Reds at Cincinnati on April 22. At Chicago the next day, Todd had a game-tying, two-run single in the eighth inning in a 6-5 Mets victory over the Cubs. He had a two-run single in the Mets’ 10-2 triumph at Atlanta on June 25. Pratt had three singles and three RBIs in a 12-8 Mets win over the Marlins at Florida on July 1. He had a pair of singles and a run scored in an 11-1 Mets victory over the Phillies at Shea on September 18. Todd also had the Mets’ biggest hit of the year with a home run in the 10th inning for a 4-3 win over the Diamondbacks at Shea on October 9 in Game 4 of the National League Division Series. This homer clinched the series for the Mets.
Pratt appeared in 80 games for the Mets in the 2000 season. He batted .275 with eight home runs in the team’s pennant-winning year. Todd had three singles and a double in the Mets’ 13-6 win at Colorado on April 29. He hit a pinch-hit grand slam in the ninth inning of a 10-5 Mets victory over the Dodgers at Los Angeles on May 30. Pratt homered in the Mets’ 5-2 triumph over the Devil Rays on June 2 at Shea. He singled twice and scored a run in a 6-4 Mets win at Boston on July 14. Todd had three singles and three runs scored in a 7-5 Mets victory over the Rockies in the first game of a doubleheader on August 15 at Shea. He also singled three times and drove in three runs in the Mets’ 8-2 win over the Braves at Shea on September 28.
In 2001, Pratt appeared in 45 games as a Met. He had 80 at bats and 24 total bases with the team during the season. Todd hit a pair of doubles in an 8-1 Mets victory over the Diamondbacks at Shea on May 5. He singled twice in a 4-2 Mets triumph on May 23 at Montreal. At Philadelphia on July 20, Pratt homered for the Mets’ only run in a 10-1 defeat to the Phillies. This was Todd’s last at bat as a member of the Mets. Three days later, he was traded to the Phils for Gary Bennett.