Allan Bryant, 23, went missing after a night out at Styx nightclub in his home town of Glenrothes on 3 November 2013.
Officers began searching the house in Barnton Place on Friday 16 June.
Police Scotland said the property had now been returned to its owners and no further investigations would be made at the house.
Det Insp Stuart Wilson, of Police Scotland, said: "Inquiries into the circumstances of Allan's disappearance are ongoing and we are committed to finding him.
"We still believe that someone in the Glenrothes area has information that will assist with our inquiries.
"I would ask that person to come forward and help us give the Bryant family the answers they are desperately seeking."
Mr Bryant's parents have repeatedly stated they believe he has been murdered and that his killer is still at large.
Police investigating the disappearance of a Fife man have ended the search of a house in Glenrothes without making any fresh discoveries.