Born in Montreuil, Prunier was a product of a famous Auxerre youth team that also included Eric Cantona, Basile Boli, Pascal Vahirua and Daniel Dutuel, all under the tutelage of Guy Roux.
Marseille were relegated to Division 2 the following season due to match-fixing and financial irregularities, and Prunier moved on to Bordeaux, where he won the UEFA Intertoto Cup in 1995 playing alongside Zinedine Zidane.
Prunier made his Manchester United debut against Queens Park Rangers on 30 December 1995 partnering Gary Neville in defence.
With Peter Schmeichel injured during the game and Denis Irwin unavailable, he was part of a makeshift defence that conceded four goals in a humiliating loss.
[5] After leaving Manchester United, Prunier moved on to Copenhagen in Denmark and also had spells at Napoli in Italy and Kortrijk in Belgium before returning to France with Toulouse where he won the Ligue 2 title in 2003.