The body was found in the rubble of a shop, gutted in the 3 June blaze, after locals complained of a foul smell.
A BBC correspondent in Accra says it raises questions about whether there could be more bodies at the site.
Ghana observed three days of official mourning for victims of the fire.
BBC Africa Live: News Updates
"Shock and mourning" after deadly fire
An official investigation, which released its report last week, found that the fire had started after a discarded cigarette came into contact with a large amount of fuel, which had leaked out of the station and mixed with pools of flood water.
Authorities in Ghana's capital Accra have recovered a body from one of the buildings destroyed in a petrol station inferno more than two months ago, in which at least 154 people died.