During World War II, Loxton served with the 2nd Armoured Division. He enlisted on 31 July 1942 at Oakleigh, Victoria and was discharged on 7November 1945 with the rank of sergeant, having spent most of his time at the division headquarters. The war ended Loxton and Miller's partnership at St Kilda. Miller was deployed to South Australia for training before becoming a fighter pilot in England, while his St Kilda colleague served in a reserve unit in Melbourne, enabling him to continue his football career when granted leave. In 1943, Loxton played in only the last four matches of the season, all of which were lost, kicking seven goals, and St Kilda finished last with a solitary victory from ten games. He managed three goals each against Essendon and South Melbourne but was held goal-less against Melbourne. The following year, Loxton played in all 18 matches and topped St Kilda's goal-kicking aggregates with 52. After making a slow start to the season, aggregating only four goals in the first four matches, including two goal-less outings, he began to score more heavily. The St Kilda forward registered a six-goal haul against Geelong in round eight, helping to secure an away win, and scored 23 goals in the last six matches, including five in each of the last three matches. However, St Kilda won only one of these three matches. Loxton's efforts helped his club to finish ninth out of 12 teams, and he came second in the club Best and Fairest. He played a solitary match in 1945, which St Kilda lost, and went goal-less.