Vukušić started his career playing at youth level for his hometown club Junak Sinj. He joined Hajduk Split in 2007, and during his time at their youth academy was regarded as one of the most promising players.
Hajduk Split
In January 2009, he signed a professional -year contract with Hajduk keeping him at the club until summer 2014. He made his debut for the first team in a 5–0 win against Croatia Sesvete on 22 April 2009. In the last round of 2008–09 season, he scored his first goal in Prva HNL, a late equalizer against rivalsDinamo Zagreb. In the 2009–10 season, Vukušić established himself as the first choice striker at the club. In 22 league appearances, he scored 6 goals and a further 2 goals in 5 cup appearances. His stature at the club at such a young age impressed many of Europe's top clubs and he was set to make a move away from the Croatian club but the management and he mutually chose for him to remain at the club for the following season. In the 2010–11 season, he scored 14 league goals in 29 appearances, finishing the season as the club's top scorer. He also scored four goals in nine UEFA Europe League appearances, the most memorable of which was a last minute winner against Anderlecht. At the start of the 2011–12 season, under new coach Krasimir Balakov, Vukušić continued as the first choice striker at the club, this time alongside new signing Ivan Vuković as the most preferred front duo. He scored his first goal of the 2011–12 Prva HNL only three minutes into the first match against Šibenik and added his second in a match against Rijeka. In doing so he injured his toe and was consequentially ruled out for the next four weeks. He ended the season with 12 league goals in 24 appearances and 15 total goals in 29 appearances which made him the top goalscorer at the club for the second year running. The 2012-13 season at Hajduk started with another new coach, but Ante remained the first choice striker and captain at the club, despite his young age. He converted a penalty in Hajduk's 2–0 win over Italian club Internazionale at the San Siro.
In August 2012, Vukušić was transferred to the newly promoted Serie A club Pescara for a reported fee of around €3.8 million. He was initially the first choice striker at the club, but ended up losing his place and managed just one goal in 19 appearances as Pescara were relegated.
He moved to Greuther Fürth on 29 January 2016. On 7 May 2016 he extended his contract until June 2018.
Tosno
On 5 June 2017, he signed a 2-year contract with the Russian Premier League club FC Tosno. Three weeks later, he underwent a surgery on his lungs, due to years-long medical problems.
