Kubina was drafted in the seventh round of the 1996 NHL Entry Draft by the Lightning. He had been playing for Vítkovice HC of the Czech Extraliga when he was drafted. He came to Canada to play for the Moose Jaw Warriors of the WHL after being drafted, and scored 44 points in 61 games. Kubina got his first taste of NHL action in the 1997-98 NHL season, although he spent most of his time playing for the Adirondack Red Wings of the AHL. He spent most of next season in the NHL, scoring 21 points, but spent a little bit of time playing in the IHL for the Cleveland Lumberjacks. Kubina was in the league for good by the 1999-00 NHL season, and put up another 26 points for the Lightning.

Kubina continued to score respectably for Tampa Bay over the next few seasons, tallying 30 points twice. He also received praise for his physical play, helped by his 6'4", 230 pound frame. He had become an important defenseman for the Lightning, but was still dogged by charges of immaturity and inconsistency. By 2003, he was widely respected, but not considered an All-Star.

He earned a spot on the Eastern Conference's roster for the 2004 NHL All-Star Game, en route to a 17 goal, 35 point season that was his best offensive season to date. He also managed to earn a +9 plus/minus, the first positive plus/minus of his NHL career. In the playoffs, Kubina showed his mettle by coming back for Game 5, missing only one game after having suffered a suspected concussion. Despite missing this game, he was third on the Lightning in playoff ice-time, and was the Tampa Bay defenseman who spent the most time on the ice in the playoffs, trailing Martin St. Louis and Brad Richards.

Pavel Kubina has proved that he is a top defenseman in the league by being the top defenseman on a Stanley Cup-winning team. He remains a vital cog for Tampa Bay, and will likely be spending several more successful seasons there.