Clune was drafted in the second round of the 2003 OHL Priority Selection by the Sarnia Sting. During the 2003–04 season, Clune scored three goals and 16 points, as well as 72 penalty minutes, in 58 games. In 2004–05, his second year with the Sting, Clune finished the season with 21 goals and 34 points in 68 games and added 103 penalty minutes, fourth most on the team, as well as winning the Bobby Smith Trophy, emblematic of the OHL's scholastic player of the year. In April 2005, Clune represented Canada at the World Under-18s in the Czech Republic; Canada won a silver medal, losing in the gold-medal game to the United States. Clune was drafted in the third round at the 2005 NHL Entry Draft by the Dallas Stars on July 30, 2005, despite not playing at the CHL Top Prospects Game in Vancouver. In August 2005, Clune yet again represented Canada in the Czech Republic, this time at the Junior World Cup of Hockey. This time, Canada won gold, winning it over the host team. Despite Clune's 20 goals, 52 points and 126 penalty minutes in 61 games in 2005–06, Sarnia finished last in the OHL standings and Clune demanded a trade. On September 20, 2006, Clune was traded to the Barrie Colts for Mike Roelofsen and three draft picks. In October, the Colts honoured Clune with the team's monthly sportsmanship award. Clune was criticized when, during a game against London on October 28, 2006, Clune scored an empty-net goal to secure a 5–3 victory and celebrated the goal by doing pushups on the ice. Clune had had his best season offensively, scoring a career-high 32 goals and 46 assists for a career-best 78 points in 67 games.
Professional
On March 25, 2007, Clune signed a three-year entry-level contract with Dallas Stars. He made his professional hockey debut on April 14 with the Iowa Stars, Dallas' AHL affiliate. Clune ended the 2007–08 season splitting time between Iowa and the Idaho Steelheads of the ECHL. On July 21, 2008, he was traded to the Los Angeles Kings in exchange for Lauri Tukonen. After suffering a chest injury at training camp on October 6, 2008, Clune wasn't assigned to the Kings' affiliate, the Manchester Monarchs, until November 19, 2008. During the 2010 playoffs, Clune made four brief appearances in their first-round loss to the Vancouver Canucks, but is noted for his fight in Game 5 with Rick Rypien. Prior to the 2012–13 lockout-shortened season, Clune was picked up off waivers from the Kings by the Nashville Predators on January 15, 2013. Having established a fourth line role with the Predators, Clune was re-signed to a two-year contract extension to begin in the 2014–15 season. Clune featured in a single game under new head coach Peter Laviolette before he was reassigned to the AHL with affiliate the Milwaukee Admirals for the duration of the year. After he was placed on waivers in the off-season with no claim, Clune was placed on unconditional waivers to buy out the final year of his contract and secure a release to free agency on June 27, 2015. On July 5, 2015, Clune signed a one-year contract with the Toronto Marlies of the AHL. Clune produced 5 points in 8 games to open the 2015–16 season with the Marlies, before he was signed to a one-year two-way contract with the parent club, the Toronto Maple Leafs, on October 29, 2015. On July 4, 2016, as a free agent from the Maple Leafs, Clune opted to continue playing with the Marlies, signing a new one-year AHL deal.
Personal life
During the 2014-15 season Clune began taking acting classes. In the 2017 offseason, he filmed roles in two short films. His younger brothers, Matt and Ben, are screenwriters. The three brothers grew up in Toronto, Ontario. Clune is of Irish and southern Italian descent. Clune has written of his near-decade-long struggle with substance addiction, and an upcoming documentary feature on his life will be released in 2020. Clune's great-uncle was Robert Clune, a bishop in the Archdiocese of Toronto.