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.[8]
Interblock Ljubljana
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[9] and a Super Cup.[10]
Al Arabi
Skočić took a year long sabbatical from coaching following his time at Interblock,[11] 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.[12]
Al Nassr
Following Kuwait, in the 2010–11 season, Skočić was engaged by the Al Nassr football club from Riyadh, Saudi Arabia, one of the most prominent football clubs in the Arab world. Under Skočić, Al Nassr qualified for the third round of the AFC Champions League, after having played a successful season of competitions within the group. On 25 May 2011, he was sacked after a disappointing 4–1 loss to 2010 AFC Champions League finalists Zob Ahan, and was replaced by Portuguese boss Eurico Gomes.[13]
Return to Rijeka
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 2011–12 Prva HNL season.[14] Skočić inherited a defensively frail side that was 2 points off the relegation zone and was tasked with saving the team from relegation.[15] Upon a 2-0 defeat to Cibalia, the club fell to the 12th place in the league.[16] After just 43 days in charge,[17] Skočić was relieved of his position, following a series of poor results, and was replaced by his assistant, Mladen Ivančić.[18][19][20]
Malavan
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.[21] He led the club to the seventh place, their best league finish since 2005.[22]
Foolad
On 23 May 2014, Skočić was named as new head coach of Iran Pro League title-holders Foolad,[23] on a one-year contract, replacing Hossein Faraki who resigned on the following day.[24] 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.[25] 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.[26] After an unsuccessful transfer to Sepahan, he remained as Foolad's head coach according to his contract.[27][28] He left the club on 1 June 2016.[29]
On 6 February 2020, Skočić was named head coach of the Iran national team.[34] He managed to take Iran to the 2022 World Cup as the winner of Group A by scoring 25 points out of 10 matches in the third round of the World Cup qualifiers and set the best performance of the Iran national football team in the World Cup qualifiers.[35][36]
He was replaced as the Iranian national team manager on 7 September 2022.[37]