The 1999 National Lacrosse League season is the 13th season in the NLL that began on December 26, 1998, and concluded with the championship game on April 23, 1999. The Toronto Rock celebrated their first season in Toronto by winning the championship, defeating the Rochester Knighthawks 13–10 at Maple Leaf Gardens.

The playoffs featured the lowest score by a team in NLL history, when goaltender Bob Watson and the Toronto Rock defeated the Philadelphia Wings 13–2.

The only change of teams from the 1998 NLL season to 1999 was the movement of the Ontario Raiders from Hamilton down the QEW to Toronto to become the Toronto Rock.

Reference: ^[1]

x: Clinched playoff berth; c: Clinched playoff berth by crossing over to another division; y: Clinched division; z: Clinched best regular season record; GP: Games Played
W: Wins; L: Losses; GB: Games back; PCT: Win percentage; Home: Record at Home; Road: Record on the Road; GF: Goals scored; GA: Goals allowed
Differential: Difference between goals scored and allowed; GF/GP: Average number of goals scored per game; GA/GP: Average number of goals allowed per game

The 1999 All-Star Game took place at the Blue Cross Arena in Rochester, where Team Canada defeated Team USA by a score of 25–24.

Bold numbers indicate new single-season records. Italics indicate tied single-season records.

• 1999 in sports