After registering six points in 39 games with the Islanders in the 2009–10 season, Thompson was claimed off waivers by the Tampa Bay Lightning on January 21, 2010. He would appear in 32 games for the Lightning, scoring one goal and three assists for four points; in total, he scored two goals and eight assists for both the Islanders and Lightning, then-career-highs. He also excelled in face-offs, winning 219 of 385 taken for Tampa Bay, a 56.9 percent success rate. In the subsequent off-season, on July 10, 2010, Tampa Bay re-signed Thompson to a one-year contract.