Manuel Baquedano was born in Santiago, the son of cavalry colonel Fernando Baquedano and of Teresa González de Labra y Ros. He studied at the school of clergyman Juan Romo and at the Instituto Nacional of Chile. During this time he became lifelong friends with Federico Errázuriz and Eusebio Lillo. Baquedano was only 15 years old and still at school when the War of the Confederation broke out. He fled his home in July 1838 to join the troops leaving for the War. He participated in the Battle of Yungay in 1839, being promoted on the field to Lieutenant at the age of 16.