Born in Kouvola, Finland, he began playing professionally at the end of the 1950s. He played in a sextet led by Heikki Rosendahl during that time, and then studied flute performance at the Sibelius Academy and in the U.S. at the Berklee College of Music. Moving back to Finland, he settled in Helsinki and began working both as a session musician and with fusion groups. Later in the 1960s he formed a duo with Edward Vesala, as well as in the group Eero Koivistoinen for four years. He recorded with Thad Jones and Mel Lewis and with Heikki Sarmanto in the late 1960s and early 1970s, and his first album as a soloist, Etiquette, was released in 1974.
In 1975, he became a member of the New Music Orchestra, and worked with the Nordic All Stars, Arild Andersen, and Peter Brötzmann later in the 1970s. The 1980s saw him working with the UFO Big Band, Jan Garbarek, Charlie Mariano, and others. He was granted a 15-year state grant from Finland in the mid-1980s. He led a touring quartet from 1990 to 1992 with Olli Ahvenlahti, Heikki Virtanen and Reino Laine. Aaltonen and Heikki Sarmanto released a duo recording, Rise, in 2001; in 2003 Aaltonen's trio album Mother Tongue won a Jazz-Emma in Finland. Aaltonen continues to teach at the annual Nilsiä Music Camp.