In a January article on SI.com, Singh admitted using deer antler spray, which contains a hormone believed to assist in muscle recovery. The substance was then on the PGA Tour's banned substance list.
However, deer antler spray was later removed from the World Anti-Doping Agency's list of banned substances. The golf tour used the anti-doping agency's list to determine its own list.
Singh's lawsuit claims the PGA Tour failed to "determine in a responsible way" whether the spray was a "banned substance" by the agency's definitions.
The PGA Tour then ended all disciplinary action against Singh, but he claims the organization tried to suspend him for 90 days. He appealed and his winnings -- about $100,000 -- were put in escrow.
"I am proud of my achievements, my work ethic and the way I live my life," Singh said in a statement. "The PGA Tour not only treated me unfairly but displayed a lack of professionalism that should concern every professional golfer and fan of the game."
The statement from Singh and his attorney didn't outline what compensation the golfer was seeking from the PGA Tour.
Singh, 50, is expected to take part in this week's PGA Tour's Players Championship. He has won three major tournaments among his 58 tournament titles and was inducted into the World Golf Hall of Fame in 2006.