The Swans revealed the shock diagnosis on Thursday, with Gowans to step away from the club for six weeks to allow him time to recover.
Gowans will undergo surgery in the coming weeks, and is expected to make a full recovery.
Assistant coach Nick Davis will take on the senior coaching duties in Gowans' absence.
Gowans had medical tests for a separate issue last year, during which an abnormality was detected.
Further investigation uncovered a tumour, which fortunately hasn't spread.
"If there's one positive to take from this it's that the tumour can be removed and hasn't spread, which may not have been the case if it wasn't discovered so early," Gowans said in a statement.
"I'm extremely lucky that my doctor pushed for further investigation into something that wasn't quite right - I didn't have any symptoms and I was otherwise feeling OK.
"What I hadn't done was have a check-up for prostate cancer, so if there's one message to come from this experience it's to get checked, and urge your loved ones to get checked, because it could save their life."
Gowans, who was axed as coach of the North Melbourne AFLW side in 2020 despite boasting a 79 per cent winning record, was appointed Sydney's inaugural AFLW coach early last year.
The squad lacked star power in its first season, with the Swans finishing on the bottom of the ladder with a 0-10 record and a percentage of 35.9.
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