The Chelsea boss is backing the Super Eagles to follow Argentina into the second round of the summer showpiece in Brazil.
Nigeria faces a difficult task, having been drawn alongside Argentina, Bosnia-Herzegovina and Iran Group F.
The Chelsea coach, speaking at a Yahoo global football ambassadors event, tipped Argentina to top the pile, but feels Nigeria is capable of joining it in the knockout stages, although admitted he is biased because his player John Obi Mikel plays for the Super Eagles.
"Argentina has to be the group winner and what makes me decide for Nigeria is the fact that I have there one player there," he said.
Mourinho was then asked for his opinion on Cote d'Ivoire, the country of his former star player Didier Drogba.
"I'm very emotional, I go always with my friends," Mourinho said in reference to his backing of the Ivorians, who will battle Greece, Japan and Colombia in Group C.
Ivory Coast begins its campaign against Japan in Recife on June 14 while Nigeria opens against Iran in Curitiba two days later.