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He became the coach of 1. FC Slovácko, replacing Josef Mazura on 18 April 2010. After losing the opening three games of the 2012–13 Gambrinus liga, Soukup was relieved of his duties. Soukup was not out of football for long, as he took over at Gambrinus liga side SK Dynamo České Budějovice in September 2012 following the dismissal of František Cipro. He didn't last long as he was sacked in the winter break of the 2012–13 season after a 6–1 friendly match loss to Mladá Boleslav in February 2013. On 13 May 2014 he was confirmed as the head coach of Yemen national football team. On 27 July 2016, Soukup was appointed as the new manager of the Bahrain national football team. Under his guidance, Bahrain progressed to the knockout stage for the first time since 2004, and it was considered as a success. Despite this, Soukup left the position after the Asian Cup.
Shortly after he was rehired by Yemen ahead of the Arabian Gulf cup