In 1936 Mitchell-Innes was elected captain of the Oxford team. The side lacked the batting strength of the previous years, and he was forced to move himself from his preferred position of batting at number three or four, to open the batting during the season. The batting suffered a further blow just prior to the University match when Roger Kimpton suffered an injury and was unable to play. Along with Kimpton, Mitchell-Innes led the batting averages by a large margin, having scored 917 runs at 43.66. He also reached his highest score in first-class cricket against H. D. G. Leveson Gower's XI, scoring 207 runs. Oxford lost more matches than they won during the season, including an eight-wicket loss to Cambridge in the University match. Despite the loss, the match was Mitchell-Innes' most successful contest against Cambridge, as he scored 43 and 84. During this season, Mitchell-Innes had his most effective spell as a bowler, taking 22 wickets for Oxford at an average of 26.27, but Bolton described the team's bowling performances as unremarkable.