Rooney had been ill for some time, US entertainment media reported. The celebrity website TMZ said that Rooney died of natural causes.
Rooney rose to fame as the plucky diminutive lad in the successful "Andy Hardy" film series of the late 1930s and early 1940s.
He also had notable turns as Puck in "A Midsummer Night's Dream" (1935) and in "National Velvet" (1944), opposite Elizabeth Taylor.
Rooney -- born Joe Yule Jr. on September 23, 1920 in New York -- more recently appeared in the 2006 comedy "Night at the Museum," and in the 2011 movie "The Muppets."
Credited with performances in more than 200 films, Rooney was awarded an honorary Oscar in 1982 for lifetime achievement.