Matthew Wilkie was born in Orange and studied at the Queensland Conservatorium of Music in Brisbane. During his studies he performed as a soloist with the Queensland Youth Orchestra on numerous occasions, and after graduating he settled in Hannover, Germany, where he continued his studies with Professor Klaus Thunemann.
In Germany, he appeared as soloist with a number of orchestras including the South West Germany Chamber Orchestra and the Württemberg Chamber Orchestra. He won second prize in the International Music Competition in Geneva where he performed the Mozart Bassoon Concerto with the Orchestra de la Suisse Romande.
Matthew Wilkie joined the Chamber Orchestra of Europe in 1986 as Principal Bassoon and has made a number of solo performances and recordings with them, including the Mozart Bassoon Concerto and the Strauss Duet Concertino. He has also recorded Mozart's Wind Serenades and Divertimenti with the Wind Soloists of the Chamber Orchestra of Europe. In 1995, together with members of the COE, he recorded the six Trio Sonatas by Jan Dismas Zelenka.
Matthew Wilkie was appointed Principal Bassoon with the Sydney Symphony Orchestra in 2000.