The following off-season, Cloutier was traded on the day of the 1999 NHL Entry Draft (June 26, 1999) to the Tampa Bay Lightning. He was sent to Tampa Bay, along with winger Niklas Sundstrom, a first-round selection (Nikita Alexeev) in 2000 and a third-round selection (subsequently traded) in 2000, for the Lightning's first-round selection in that year's draft (Pavel Brendl). With the departure of Tampa Bay's previous starter, Bill Ranford, to the Detroit Red Wings and Darren Puppa nearing the end of his career, Cloutier assumed the starting position for his new club. Cloutier's first season as an NHL starter was interrupted on several occasions with numerous injuries and a suspension. He suffered a strained groin early in the campaign on November 18, 1999, forcing him out of two games. On January 14, 2000, he was suspended by the league for four games after an incident with Islanders forward Tim Connolly. After the two collided, Cloutier cross-checked Connolly, then kicked his head (Connolly's helmet was intact) while he was lying face-down on the ice. The following month, he re-strained his groin on February 21 and missed four games. Cloutier missed another four contests beginning on March 14 after injuring his neck. His fourth injury of the season occurred on March 28, when he strained his medial collateral ligament (MCL) and missed five games. He finished the 1999–2000 season appearing in 52 games for the Lightning, recording 9 wins, 30 losses and 3 ties as the team finished second-last in the league. He registered a 3.49 GAA and .885 save percentage.