His influence as club captain was later transferred to management as he re-joined Leicester City once more, this time as manager after the end of World War II. He managed the club to their first ever major cup final, the 1949 FA Cup Final, which they lost to Wolverhampton Wanderers. The run to the cup final included an incredible 5–5 draw with Luton Town in the 5th round, in which Jack Lee managed to head home a Mal Griffiths corner in injury time of extra-time (this was Lee's fourth goal of the match) to equalise and send the game to a replay. Duncan missed the goal as he was on his knees with his back to the pitch, praying in desperation.