The 53-year-old actor was at the St. Regis hotel in San Francisco on Tuesday (19.11.13) when he started shouting at the man who appeared to be using his mobile to snap a picture of the star.
A video posted by TMZ shows the two-time Oscar winner appear to lose his temper in the lobby of the hotel in the city's Financial District.
A witness said the 'Secret Life of Walter Mitty' actor lunged at the man - who wasn't believed to be a paparazzi photographer - and screamed, "Do we look like f**king zoo animals?"
In the video, he is then seen gesturing at the man and shouting: "I'll make you eat the phone ... Get the f**k out of here. Get out of here!"
He is said to have then thrown the fan's phone on the ground before telling the hotel's manager, "You should do something about that."
It has been reported the fan was asked by staff if he wanted to call the police but he said no and left.
The fan was attending the same conference as the actor and was wearing his name badge from the event during the bar altercation.
Sean is well-known for having a temper and has was sentenced to 300 hours of community service in 2010 after allegedly kicking a photographer.
He served 60 days in prison in 1987 for punching a movie extra in the face numerous times when the man took photographs of him on the set of drama Colors.
In the same year, he was charged with domestic assault after hitting his then wife, singer Madonna, across the head with a baseball bat.