Documented references to the comune of Villapizzone date back at least to 1346. In the late middle ages and until the 18th century, the comune used to be part of the pieve of Trenno. During Napoleonic rule, Villapizzone was annexed to Milan, but regained its autonomy with the Kingdom of Lombardy-Venetia. In 1869 it was annexed to Musocco, which in turn became part of Milan in 1923.
Villapizzone remained a rural district until World War II; thereafter, it became part of a seamless residential area that includes Bovisa, Quarto Oggiaro and several other districts. The toponymy "Villapizzone" itself was scarcely used for several decades; it reappeared in the late 20th century as a consequence of the realization of the Villapizzone railway station.