Huddersfield Town's 1945–46 campaign was mainly played in the still active Wartime League, but the FA Cup was revived for the 1945–46 season in a two-leg format.

Town went out in the third round to Sheffield United.

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Town were out in Round 3 with a 1–1 draw at Leeds Road, followed by a 2–0 loss at Bramall Lane, which made them lose 3–1 on aggregate.