The 25-year-old was drawn into a fiery exchange in front of his 573,000 followers, and warned he would put the fan "asleep within 10 seconds" if he showed up at United's training ground.
The exchange began when the fan, Liverpool supporter Sam Oldham, said, "Rooney ya fat whore ill smash ya head in with a pitchin wedge an bury ya with a ballast fork ya fat ugly lil nonse."
The England international responded, "haha you know were I train every day kid come and do it good luck.''
Oldham, whose account has since been deleted, then said, "and ill be down tomorrow lad in me twin turbo nissan micra."
Rooney replied, "I'll put u asleep within 10 seconds u little girl. Don't say stuff and not follow up on it. I'll be waiting."
The United star later played down the incident, tweeting, "Haha bit of banter and people go nuts chill all people."
Meanwhile, it appears Rooney has had enough of taunts from CNN talk show host Piers Morgan, who has repeatedly criticized his poor grammar and spelling on the microblogging site.
After Rooney used Twitter to congratulate his teammates Nani and Javier Hernandez for being named Players' Player and Fans' Player of the Year respectively at Manchester United's official awards night, Morgan responded, "What award did you win @WayneRooney - Fastest Transfer U-Turn of the Year After Big Cheque Arrived?"
Rooney responded, "@piersmorgan did u win 1 for most boring show of the year. Stop hanging on to me pls. I don't want to know u."