Lee Lynch began his playing career with former Limerick club Roxboro United, followed by Summerville and finally Regional United where he played until the age of 16. He won two All-Ireland senior soccer titles with Limerick CBS. From there he moved to England to sign for West Bromwich Albion. He played an important role with the youth team there and progressed to play for their reserves where he made 20 appearances. After two years he left in 2010. He then moved to Spain and signed with the Glenn Hoddle Academy playing with Jerez for the 2010-11 season.
Professional
Drogheda United
Lynch returned home to Ireland in July 2011 to sign for Drogheda United midway through the season. He played every game until the end of the season scoring four goals from 14 games. He was named Fans' Player of the Year as he helped them keep their Premier Division status that season.
Lynch's performances in Drogheda didn't go unnoticed and he signed for top four team Sligo Rovers on 6 January 2012. Aged 19 he quickly established himself in the first-team scoring his first goal against Bohemians in the third game of the season to give his new club a 3-0 win. He helped the club to win the league that season missing only three games and contributing three goals. He made 36 appearances in all competitions scoring four goals. After missing the first game of the 2013 season against Derry he started every league game after that scoring against Cork City and Derry City. He also scored three goals over two legs to help Rovers into the Setanta Sports Cup semi-final. Lynch had two successful seasons with Sligo Rovers winning the 2012 League of Ireland and the 2013 FAI Cup. It was during his premier season with Sligo when Lynch made his debut in Europa Cup again Sparta Moskva, narrowly losing out over two legs home and away. In 2013 following their league winning season, Lynch featured again Europe, this time in the Champions League qualifier, where he featured against FC Molte from Norway
Lynch signed for Hamilton Academical on 3 January 2015 after the international transfer window opened. He was released by Hamilton in March 2015.
Limerick
On 3 July 2015, Lynch signed for Limerick for a third time. Lynch played a pivotal part in helping to return Limerick FC to the Irish Premier league, scoring 10 goals from midfield and picking up fans' player of the year. Lynch was central in helping Limerick FC make it to the final of the EA sports cup. Despite scoring in the final to give Limerick FC a one nil lead at half time, St Patrick's Athletic ran out winners.
Lynch joined Larne in January 2019 and helped the club to the 2018/19 Championship title.
International
Lynch has two underage caps for Ireland coming at under-17 level. He scored twice on his debut against Finland. He has also been called up to under-18 and under-19 squads.