Due to an internal conflict he left the club after one season to pursue a career as a manager. He began his career as a manager in third tier club NK Orijent in Rijeka. He took the club to the quarter final of the 1981 Yugoslav Cup beating NK Zagreb and OFK Beograd. In the quarter final Orijent lost to Budućnost Titograd of penalties. Skoblar joined NK Rijeka in May 1983 replacing Marijan Brnčić. He concluded the last six matches of 1982–83 season and saved the club from relegation and finished at 15 place. In his second season at the club Skoblar nearly won the League short three point from first placed Red Star Belgrade, Rijeka finished in fourth place behind Željezničar and Partizan. This result was the club best league result since 1965–66, they also reached the quarter final of Yugoslav Cup and qualified for UEFA Cup. On 24 October Rijeka beat Real Madrid 3:1 in the second round of the UEFA Cup. This match made Skoblar reputation with the supporters and club rise to a status of legend. In their away match against the Spanish side they lost 3:1 with Real Madrid advancing and eventually winning the Cup. Many of the players and Skoblar himself have stated that they were cheated from victory by the referee. The season ended with the club at a mid-table eight place, four points shy of a European qualification.   1985–86 season started out poorly with losses in the league and elimination in the second round of the Cup. During the second part of the season Skoblar managed to secured fifth place with the club and secured a place in the UEFA Cup. Rijeka was eliminated during the first round of the 1986–87 UEFA Cup by Standard Liège. Mid-season Rijeka was in tenth place in the league and had reached the semi final in the Cup. Skoblar left the club in December 1986. He later became head coach for Hajduk Split with whom he won 2 Yugoslavia Cups. With Hamburger SV he lost DFB Supercup in 1987. In 1988 he managed Čelik Zenica and saved them from relegation. He also had short stints in Spain with Real Valladolid and Portugal with F.C. Famalicão. He also coached Croatian clubs Dinamo Zagreb, NK Zagreb, Zadarkomerc and HNK Rijeka.