Cancellara was born in Wohlen bei Bern, a municipality near the city of Berne, Switzerland to Italian parents that had emigrated from San Fele. He discovered cycling at the age of 13 after falling in love with an old family bike that he had found in the garage and immediately gave up football to concentrate on cycling.
Cancellara's cycling skills began to blossom at an early age, when he impressed as a time trialist and dominated Swiss junior cycling. Yvan Girard, Swiss national junior team coach from 1997 to 2005, was quoted saying that Cancellara was head and shoulders above everyone else in the time trials. He won the junior World Time Trial Championship in both 1998 and 1999 and at the age of 19 he came in second at the 2000 U-23 World Time Trial Championship, after which he turned professional with Mapei-Quick Step, then one of the strongest teams in the world.