The film is a fictionalized account of the founding and early years of the "Boys Town" organization for troubled boys. Tracy plays Father Edward Flanagan, who starts the movie running a refuge for hobos, but comes to believe that his time would be better spent mentoring troubled boys before they become hardened toughs. Father Flanagan takes five local street kids into a home. When the five kids grow to be fifty kids Father Flanagan builds an institution that becomes known as "Boys Town". Mickey Rooney plays Whitey Marsh, a particularly troubled kid that Father Flanagan takes a special interest in.
Boys Town received five Academy Award nominations and earned Tracy his second of his back-to-back Best Actor awards.
- Blackface: One of the kids, working as the barber, plays a prank on Whitey, smearing his face with shoe polish when Whitey thinks he's getting a facial massage.
- Chromosome Casting: Boys Town didn't start admitting girls until 1979. Exactly one woman has exactly one line in the movie—a nun working in the infirmary where Pee Wee is being treated.
- Contrived Coincidence: A distraught Whitey is aimlessly wandering the streets of Omaha after Pee Wee is hit by a car and injured. He walks right into a bank robbery being perpetrated by his older brother Joe, an escaped convict.
- Extra! Extra! Read All About It!: "Read all about it! Dan Farrow electrocuted!"
- Good Shepherd: Father Flanagan, working tirelessly to save troubled and deprived boys.
- Good Smoking, Evil Smoking: The movie had to work hard to make the audience believe that apple-cheeked, all-American Mickey Rooney, Andy Hardy himself, was a tough kid. So when he's introduced, he's smoking a cigarette and playing poker with his buddies.
- Had to Come to Prison to Be a Crook: Father Flanagan is partially motivated by a visit to Dan Farrow, a convict that is minutes away from execution. Farrow says that if someone had been a friend to him when he was a child, things might have turned out differently. Instead he went to reform school, where his criminal skills were escalated from stealing bread to bank robbery.
- Little Brother Is Watching: Whitey idolizes his older brother Joe, who is in prison for murder. Joe contacts Father Flanagan, asking him to take in his little brother so he won't follow the same path.
- Match Cut: As Whitey and Freddie are about to start fighting each other, Father Flanagan decides they should settle their differences in the ring. Cut to Whitey, Father Flanagan, and Freddie, in the exact same position, but in the ring as their boxing match is about to start.
- Mouthy Kid: Whitey
- Rousseau Was Right: Father Flanagan's firm belief that he could turn any boy around, as reflected in the page quote. (Luckily the real Father Flanagan didn't live long enough to find out that Charles Manson briefly stayed at Boys Town.)
- Sliding Scale of Idealism vs. Cynicism: They don't make them more idealistic than this one.
- Very Loosely Based on a True Story: As the opening credits note, Father Flanagan was a real guy and Boys Town is a real place, but everything else was fictional.