Karrer was born in Moscow, Russia to Paul Karrer and Julie Lerch, both Swiss nationals. In 1892 Karrer's family returned to Switzerland where he was educated at Wildegg and at the grammar school in Lenzburg, Aarau, where he matriculated in 1908. He studied chemistry at the University of Zurich under Alfred Werner and after gaining his Ph.D. in 1911, he spent a further year as assistant in the Chemical Institute. He then took a post as chemist with Paul Ehrlich at the Georg Speyer Haus, Frankfurt-am-Main. In 1919 he became Professor of Chemistry and Director of the Chemical Institute.