Aapo Häkkinen studied harpsichord under Elina Mustonen, Bob van Asperen, and Pierre Hantaï. He completed his soloist diploma in Amsterdam in 1998. Shortly thereafter, he won second prize and the Belgian Radio and Television Prize at the Bruges Harpsichord Competition, as well as the North German Radio Musikpreis Special Prize for his interpretations of Italian music.

Häkkinen gave his first concert in 2000. He has performed as a soloist and conductor with many orchestras (including the Helsinki Philharmonic Orchestra, Tampere Philharmonic Orchestra, Musica Aeterna, Orchestra del Teatro Olimpico di Vicenza, Orquestra Metropolitana de Lisboa, Dunedin Consort) in most European countries, Israel, Turkey, Georgia, Japan, China, South Korea, Vietnam, Brazil, Colombia, Mexico, and the United States. From 2002 to 2004, he served as Christophe Rousset’s assistant at the Ambronay and Leipzig opera houses. He made his debut as an opera conductor at the Croatian National Opera in 2004.

Aapo Häkkinen has made numerous recordings for the Aeolus, Alba, Avie, BelAir, Brilliant Classics, Cantus, Deux-Elles, Naxos, and Ondine labels and has edited a series of publications on 17th-century Florentine keyboard music for Ut Orpheus Edizioni. He has been the artistic director of the Helsinki Baroque Orchestra since 2003.