On 14 April 1989 he was elected a member of the Central Committee and the Presidency of the 13th Congress of the League of Communists of Yugoslavia from Kosovo.
On 3 April 1990 he and a number of other ethnic Albanian members of the Provincial Executive Council, including one of the two vice-premiers, offered their resignations, in protest at Slobodan Milošević’s measures in the region, and the handling of the separatist unrest by the local Communist Party of Kosovo.
At the 23 May session the Kosovo Assembly rejected these resignations, and the officials continued in their posts.
Zejnullahu was later involved in the declaration of secession of July 2, 1990, after which Kosovo's Assembly and Executive Council were dissolved.
He was later designated Prime Minister-in-exile of Kosovo's shadow provincial government, and arrested for his pro-independence activities.