Marko Ylönen studied the cello with Csaba Szilvay at the East Helsinki Music Institute, with Erkki Rautio and Heikki Rautasalo at the Sibelius Academy and with Heinrich Schiff in Basel. Ylönen made the final round of the Turku Cello Competition at the age of fifteen. He received second prize in the Nordic Cello Competition in Turku in 1990 and a prize in the Tchaikovsky competition in Moscow in the same year. In spring 1996, he won the Concert Artist Guild competition in New York.

Marko Ylönen has appeared in solo recitals and as a chamber musician in several European countries, in the USA, in Australia and in New Zealand. He was the principal cellist of Tapiola Sinfonietta in 1990-91 and first solo cellist with the Finnish Radio Symphony Orchestra from 1991-1993. From 1995-2001 he played cello with the New Helsinki Quartet. Since 2000, he has been a tenured teacher of cello and chamber music at the Sibelius Academy. He was Artistic Director of the Korsholm Music Festival in summer 2004.

In addition to the classical core repertoire, Marko Ylönen frequently performs contemporary music. He has premiered several Finnish compositions, such as Jouni Kaipainen's Cello Concerto in 2003 (subsequently recorded for Ondine, ODE 1062-2). Further recordings feature Marko Ylönen with the Cello Concertos of Einojuhani Rautavaara (ODE 819-2) and Rodion Shchedrin (ODE 955-2). Marko Ylönen plays a Matteo Goffriller cello.