After one year with the Whites, he joined league rivals Bath City, but soon left to sign a contract with Southend United.

[3] Clohessy moved to Gillingham in 2005 to continue his development, as he went on to make his professional debut in a Football League Trophy tie with Wycombe Wanderers on 22 November 2005.

[5] He didn't feature for the club for one month until he came on as a half-time substitute for Jon Wallis on 26 December in a 1–1 draw with Bristol City.

[14] In September 2008, Clohessy was allowed to leave Gillingham and join Conference Premier side Salisbury City on trial.

[19] He scored his second goal of the campaign on 30 October, doubling the lead in a 2–0 win over Crawley Town, ending the club's run of seven straight defeats.

[22] Clohessy announced in March 2009 that he expected to leave Gillingham at the end of the 2008–09 season, owing to his strained relationship with Gills manager Mark Stimson.

[34] However, on 13 July, it was reported that Clohessy had attracted interest from an unnamed Football League club, and Bath manager Adie Britton said that the player would be free to leave Twerton Park.

With the club under a transfer embargo,[36][37] he and 16 other players were registered with the Football League on the eve of their opening fixture for the 2010–11 season against Stockport County on 7 August 2010.

[40] Despite carrying a slight groin strain, Clohessy put in some assured performances at full-back, and believed shaking off his niggling injury helped him to hit top form for his club.

[43] Having ended his debut season with the club with 51 appearances to his name, manager Paul Sturrock rewarded Clohessy with a two-year contract extension to keep him at Roots Hall until 2013.

[47] The 2012–13 season continued in similar fashion for Clohessy, holding down a regular starting berth as he registered his first goal of the campaign in a 3–1 win over Cheltenham Town on 15 September 2012, netting the equaliser.

They lost the match 2–0 as new manager Phil Brown in only his third game in charge led the team out at Wembley as former boss Paul Sturrock sat in the stands.

A spokesman for Southend claimed that the player was indeed in negotiations with the club for several months, with both verbal and written offers made and turned down.

[68] Inconsistent performances led to Clohessy being replaced by youngster Ross Barbour in the second half of the season, and he struggled to regain his first-team position.

[69] Clohessy returned to Essex on 1 July 2014, signing a two-year deal with League One club Colchester United on a free transfer.

[70] He was named as club vice-captain to Magnus Okuonghae on 7 August,[71] before making his debut in the opening game of the 2014–15 season in Colchester's 2–2 home draw with Oldham Athletic.