After his playing career, Skočić went on to complete the Football Academy at the Croatian Football Academy and the Coach Education and Training Department at the Zagreb Faculty of Kinesiology, receiving an UEFA-PRO Coach diploma and a Professional Bachelor of the Coaching Profession.
Rijeka
He became manager of his hometown club, Rijeka, in 2005. Skočić secured one trophy for the club, winning the Croatian Cup for the 2005–06 season.
In 2007, he became the head coach of the Slovenian club Interblock Ljubljana, while the club was in a difficult situation on the league scale. Only two years after the club was founded and under the management of Skočić, the club achieved outstanding results in the Slovenian PrvaLiga. Not only did they manage to stay in the first league, but they also won two trophies in the 2007–08 season, the Slovenian Cup and a Super Cup.
Al Arabi
Skočić took a year long sabbatical from coaching following his time at Interblock, and in the 2009–10 season, he took over the management of the Al-Arabi club in Kuwait. Under his leadership as head coach, the club played in two finals, the Crown Prince Cup and the Federation Cup. Also under Skočić, Al-Arabi played in the AFC Cup quarter-finals.
In March 2012 Skočić returned to take over the management of his hometown club Rijeka by replacing Ivo Ištuk as head coach, and became the third coach to take charge of the club in the 2010–11 Prva HNL season. Skočić inherited a defensively frail side that was 2 points off the relegation zone and was tasked with saving the team from relegation. Upon a 2-0 defeat to Cibalia, the club fell to the 12th place in the league. After just 43 days in charge, Skočić was relieved of his position, following a series of poor results, and was replaced by his assistant, Mladen Ivančić.
On 26 May 2013, Skočić was announced as head coach of Malavan for the upcoming season. He signed a two year contract with the club. He led the club to the seventh place, their best league finish since 2005.
On 23 May 2014, Skočić was named as new head coach of Iran Pro League title-holders Foolad, on a one-year contract, replacing Hossein Faraki who resigned on the following day. In May 2015, Skočić received the award for coach of the month and signed a two-year contract extension to keep him at the club until July 2017. In November 2015 after poor scores with the club, Skočić was linked with the vacant head coach position at Sepahan F.C. but the job went to his compatriot, Igor Štimac. After unsuccessful transfer saga to Sepahan, he remained as Foolad's head coach according to his contract. He left the club on 1 June 2016.
On 16 January 2018 he became manager of Khooneh be Khooneh replacing formerly resigned Javad Nekounam. He soon went on an invincible streak by getting 13 points out of his first 5 games and also leading the second tier team into Hazfi Cup's final.
