The song is about two boys ("Me and Julio") who have broken a law, although the exact law that has been broken is not stated in the song. When "the mama pajama" finds out what they have done, she goes to the police station to report the crime. The individuals are later arrested, but released when a "radical priest" intervenes.
The meaning and references in the song have long provoked debate. In a July 20, 1972 interview for Rolling Stone, Jon Landau asked Simon: "What is it that the mama saw? The whole world wants to know." Simon replied "I have no idea what it is... Something sexual is what I imagine, but when I say 'something', I never bothered to figure out what it was. Didn't make any difference to me." This implies that Simon left the crime up to the imagination of the listener, allowing each person who listens to the song to draw their own conclusion from their own thoughts and experiences. This has not stopped speculation on a definite interpretation: commentators have detected references to recreational drug use, and believe that the mother saw the boy buying drugs. More recently, in October 2010, Simon described the song as "a bit of inscrutable doggerel", while the "radical priest" has been interpreted as a reference to Daniel Berrigan, who featured on the cover of Time on January 25th, 1971, near when the song was written.
The percussion sound in the song, unusual for American pop, was created with a Cuica, a Brazilian friction drum instrument often used in samba music.
In 1988, Simon released a video for the song to promote his greatest hits compilation Negotiations and Love Songs. The video was filmed at Mathews-Palmer Park in Hell's Kitchen, which was standing in for Halsey Junior High School in Forest Hills, Queens, the neighborhood in which Simon grew up and met Art Garfunkel in high school. Many of the children featured in the video were from that same school.