The Humane Society filed a lawsuit in August after the Transit Authority declined to run the ads. The Humane Society said the pictures depict "pigs suffering in extreme confinement, a common pork industry practice."
The group says breeding pigs are often kept inside two-foot wide metal cages for most of their lives.
In rejecting the ads, the Transit Authority said they were too negative. In its lawsuit, the Humane Society said its constitutional free speech rights were violated.
As part of the settlement, the ads will run on two buses for six months.