Karttunen's repertoire ranges from the early baroque to living composers and improvisation. He has performed with many orchestras in Europe, Asia, and the Americas, including the Philharmonia, BBC Symphony, Orchestre de Paris, Filarmonica della Scala, RAI Torino, Munich Philharmonic, Royal Concertgebouw Orchestra, NHK Orchestra, Tokyo Symphony, Shanghai Symphony, Hong Kong Sinfonietta, Boston Symphony, Philadelphia Orchestra, Los Angeles Philharmonic, Simón Bolívar Symphony Orchestra, and Filarmónica de Buenos Aires, and at major festivals worldwide.
Karttunen regularly performs with various chamber ensembles, including the Sons of Chipotle with John Paul Jones, the Zebra Trio with violinist Ernst Kovacic and violist Steven Dann, a cello-piano duo with Nicolas Hodges, and the Tres Coyotes with Magnus Lindberg and John Paul Jones.
From 1994 to 1998 Karttunen was the artistic director of the Avanti! Chamber Orchestra. He has been artistic director of the Helsinki Biennale (1995, 1997), the Suvisoitto-festival in Porvoo, Finland (1994-1997) and the Musica Nova Helsinki Festival 2015. He was principal cellist of the London Sinfonietta from 1999 to 2005.
Since 2008 Karttunen has directed the Creative Dialogue workshop, which he created with Kaija Saariaho, Magnus Lindberg. Creative Dialogue took place first in Santa Fe, NM and Järvenpää, Finland and more recently at Château de Beauchêne, France and Wanantaka Manor, Finland. Karttunen teaches at the Ecole Normale de Musique de Paris.