McCowan was first selected in a Queensland representative side in 1893 and made 24 appearances for his state up till 1900. He captained the Queensland side in their tour match against Matthew Mullineux's first British Lions to tour Australia in 1899 to a surprise 11–3 victory. He captained Queensland on six other occasions and made appearances against touring New Zealand sides in 1893, 1896 and 1897. New Zealand dual-international George Smith came up against McCowan on the latter of these tours and was reported in "The Cynic" to have said "If it had not been for McCowan's fine play we would have put up much bigger scores than we did. He is the best fullback we have seen over here - kicks with either foot and is a very sure tackler - I know it".