Wilson initially competed in single-seater racing, winning 17 of 22 races to take the T Cars Championship in 2002, before a season in the Formula Renault UK Championship in 2003 for Manor Motorsport. His transition to rallying began that same year when he co-drove his father at the 2003 Malcolm Wilson Rally — and they won. His first WRC start followed in 2004 at the Wales Rally GB, where he finished 13th overall.
In 2005, Wilson was selected as one of only six competitors for the Motor Sports Association British Rally Elite training scheme for young British talent. That year he became the youngest ever winner of a British Rally Championship round, taking the Trackrod Rally at age 18. A serious crash on the Rally of Wales in April 2005 — which broke his right wrist, left forearm, and damaged his right knee — interrupted his season, but he recovered to finish seventh overall in the British Rally Championship.
Wilson joined the Stobart VK M-Sport Ford team for a full WRC season in 2006. He finished every round of the 16-event calendar, a feat no other driver managed that year. At the Rally Argentina he became the youngest driver ever to win a WRC stage, setting the fastest time on the Cordoba Stadium superspecial stage — a record later broken by Andreas Mikkelsen. He ended the year 28th in the championship with a single point.
Malcolm Wilson had structured a five-year development plan for his son beginning in 2006. In 2007, with Jari-Matti Latvala and Henning Solberg taking Stobart's manufacturer points responsibilities, Wilson was able to drive with less pressure. He finished eleventh in the drivers' world championship with eleven points. His standout result was fourth place at the 2007 Rally Japan.
In 2008 Wilson adjusted to new cars and co-driver changes. He scored his first points of that season with a sixth-place finish in Mexico. He also won the Colin McRae Forest Stages Rally in Scotland, part of a memorial tribute event for the late champion who had died in 2007.
Wilson competed for the privateer Go Fast Energy World Rally Team in 2012 alongside Henning Solberg, driving a Ford Fiesta RS WRC. After finishing 11th at the Monte Carlo opener, a broken ankle sustained in training kept him out for several months. Later that year, he secured local sponsorship from Cumbrian businesses to enter the 2012 Wales Rally GB, finishing eighth and banking four championship points.
Matthew Wilson represented one of the few true father-son pairings to reach WRC level, carrying forward the Wilson family's deep connection to Ford rally machinery and M-Sport. His 2006 season — finishing every round in a learning year — was indicative of a methodical approach to development instilled by his father's program. Though injuries and funding constraints limited his highest-level results, his fourth at the 2007 Rally Japan remained a creditable benchmark in a highly competitive field.