In 2013–14 Wilkinson started out the season playing regularly. Out of Connacht's first 12 matches in the Pro12, he started 10 and made a substitute appearance in another. Wilkinson also started all six of Connacht's games in the 2013–14 Heineken Cup, including a victory over four-time Heineken Cup winners Toulouse. In Connacht's final match of the pool stages away to Saracens, Wilkinson was forced to leave the field and be replaced due to injury. On 26 March 2014, it was announced that Wilkinson was retiring from rugby due to a neck ligament injury sustained against Saracens, having played for Connacht 183 times.