The Toronto Lynx announced its expansion rights in Toronto on June 24, 1996, and played their first A-League game in Jacksonville, Florida, on April 12, 1997. The Toronto Lynx set an A-League record of 10 consecutive wins during their first season in 1997. In 2000, the Lynx proceeded to the Eastern Conference Finals and only a 1-0 loss to the Rochester Raging Rhinos kept the Lynx out of the A-League Championship game. Despite these temporary successes, over the years it spent in the A-League (later renamed USL-D1), the team fared relatively poorly on the field and ultimately failed to consistently draw crowds of more than about 2000 people.
Peter Pinizzotto was the Toronto Lynx head coach from 1997 to 2003. The team made one playoff appearance under his reign. The next season he would be hired as assistant coach for rivals Montreal Impact. In September 2003, Duncan Wilde was appointed as the new Toronto Lynx head coach for the 2004 season bringing a new philosophy and vision for the club. Wilde also holds the position of Director of the Toronto Lynx Premier Soccer Academy and Super Y-League Program for accomplishing the mission of developing and inspiring youth soccer talent in the Greater Toronto Area. After just one season, Wilde resigned from his head coaching position amidst rumours of owner interference in squad selection. During the 2005 season the team was managed by former Lynx goalkeeper Hubert Busby Jr., though Wilde returned as head coach for the 2006 season. In their debut season in the Open Canada Cup Wilde led the Lynx to the final of the tournament, but were defeated 2-0 by Ottawa St. Anthony Italia.
During their time in the A-League and USL First Division, the Lynx were noted for developing a number of notable players, but failed to retain most of them for long, leading to poor results in the league standings.
On October 10, 2006, the Lynx announced they were voluntarily relegating themselves two levels, to the USL Premier Development League. The reasons for this were never fully revealed, but it was most likely due to their low attendance (the lowest in the USL 1st Division at that time) and the fact that Major League Soccer expansion franchise Toronto FC would be arriving the next season.
Toronto's first year in the PDL was a difficult one; they lost their opening game 3-0 to West Michigan Edge, and didn't pick up their first win until the fifth game of the season, a 2-0 defeat away at the Indiana Invaders. The Lynx's main problem was inconsistency, especially away from home, where they suffered several difficult defeats, including a 4-0 thrashing at the hands of Michigan Bucks, and a 3-1 defeat to Cleveland Internationals in early August. Their home form was generally much better, and they enjoyed several excellent results, notably a comprehensive 5-0 win over Indiana Invaders that included a 2-goal haul for Murphy Wiredu, and a 5-1 revenge win over Cleveland in which Wiredu scored another brace. An unexpected 3-1 victory over divisional champs Michigan on the final day of the season ended the year brightly; they finished in fourth place, just six points off a playoff spot. The prolific Murphy Wiredu was the Lynx's top scorer, with 10 goals.
Toronto built on their 2007 form with a generally better season in 2008. They overpowered Fort Wayne Fever 4-1 in their opening fixture in front of over 1,200 fans, and enjoyed a scintillating run of form throughout the month of June, picking up five wins two ties in nine games, including a breathless 3-2 win over West Michigan Edge in which they scored twice in the last two minutes, and a strong 1-0 win over the eventual divisional champions, Michigan Bucks. Despite a pair of impressive back-to-back 4-0 wins over Indiana Invaders and Cincinnati Kings in the run-in - the last of which saw all four goals being scored by Daniel Revivo - Toronto's final day defeat to Michigan left them in third place in the Great Lakes division, squeaking into the playoffs on 'games won' ahead of Des Moines Menace, but needing to negotiate a preliminary 'Divisional Round' play-in game against Cleveland Internationals. Unfortunately for the Lynx, Cleveland scored a late winner to take the game 2-1, sending the Ontarians home early. Daniel Revivo was Toronto's top scorer, with 9 goals on the season, while Welshman Lloyd Grist contributed 4 assists.
This list of notable former players comprises players who went on to play professional soccer after playing for the team in the Premier Development League, or those who previously played professionally before joining the team.