A striker, Heffernan played for several clubs in Great Britain which include Sheffield Wednesday, Doncaster Rovers, Notts County, Bristol City, Kilmarnock, Hibernian, Dundee, Queen of the South, and Dumbarton.

Heffernan started his football career at Notts County and at age 18, he made his league debut, coming on as a substitute for Kevin Rapley in the 76th minute, in a 1–0 loss against Oldham Athletic on 24 April 2000.

[4][5] Shortly after this, Heffernan, whose contract expired at the end of the 2003–04 season, rejected a two-and-a-half-year deal on improved terms with the club.

[9] Heffernan made his debut, in the opening game of the season, in a 1–1 draw against Torquay United on 7 August 2004 and then scored his first goal against Stockport County in his fifth appearance for the club.

[10] But the next day, Heffernan scored in a FA Cup match against Brentford, but the team lost in a penalty-shootout after a 1–1 draw in regular time.

[11] However, during the season due to injury [12] and the form of Steve Brooker and Leroy Lita,[13] his chances in the first team were limited.

Heffernan was involved in the squad in the League Cup that reached the quarter-finals, starting off beating Manchester City in a penalty shoot-out after a 1–1 draw after extra-time.

[20] Heffernan played a vital role when he scored twice in each leg of the Football League Trophy semi-final against Crewe Alexandra, goals which ultimately sent Rovers to the final of that competition.

[23] He made his return just in time for the Football Trophy final and scored the second goal at the Millennium Stadium in Cardiff against Bristol Rovers, which Doncaster won 3–2.

[25] Later in the season, Heffernan sparked a moment of controversy in the 2008 League One Play-off semi-final playing against Southend United, when he headbutted an opponent due to frustration in the final minute of the match.

Heffernan was subsequently sent-off and was unable to play in the second leg, or the final against Leeds United at Wembley Stadium.

Heffernan reflected on his incident, quoting: I was suspended for the final at Wembley because I got sent off in the semi-final first leg, so that wasn't great.

It was a bad day for me and it also involved Celtic's Charlie Mulgrew, who was playing for Southend at the time, on loan from Wolves.

[28] Eventually, the move didn't happen and Heffernan fought his way to earn a first team place and went on to make 33 appearances and scored 10 goals, finishing as the club's top scorer in all competitions.

In the 2009–10 season, Hefferman mostly spent time on the bench, coming on as a substitute in a number of games after struggling to hold down a regular place.

However, Heffernan struggled to earn a first team place at the club, having spent time on bench behind Gary Madine, Clinton Morrison and Neil Mellor.

[43] His good form continued as he went on to score a hat-trick in the Scottish League Cup third round match against Queen of the South in a 5–0 win.

[54] On 30 August 2013, it was announced that Heffernan had agreed a deal with Kilmarnock's Scottish Premiership rivals Hibernian until the end of the 2014–15 season.

Heffernan sustained a thigh injury in a goalless draw against St Mirren, where he played six minutes under new manager Terry Butcher and would be out for three-four weeks.

[74] After leaving the Dumfries club on 11 January 2016, Heffernan then signed for fellow Scottish Championship side Dumbarton on 10 March 2016, on a deal until the end of the season.