"We have analysed the play and results of the first three matches of this season along with nine games of last season and we have come to this decision," the club's president Miguel Archanco said in a statement.
It was the first sacking of a manager in Spain's top flight this season.
The club's board took the decision "unanimously", the statement said.
Archanco said the club had four possible replacements in mind, but did not name them. He added that assistant coach Alfredo Sanchez will take charge until one is chosen.
Mendilibar's sacking followed the Pamplona club's 3-0 home defeat to Villareal on Saturday and earlier defeats to Athletic Bilbao (2-0) and Granada (2-1).