Clarks has since removed Dolly Babe from its website but it is still on sale online on sites that include John Lewis and Amazon, the BBC reported.
The brand has apologised "for any offense caused" in a statement.
Nicola Sturgeon, first minister of Scotland, has tweeted that the incident is "almost beyond belief".
It is almost beyond belief that in 2017 a major company could think this is in any way acceptable. Shows what we are still up against. https://t.co/3C7Nop8o1E— Nicola Sturgeon (@NicolaSturgeon) August 13, 2017
This is not the first time Clarks has faced controversy over its school shoe ranges. Last summer the brand promised to revamp its school shoe ranges after parents complained that its shoes for girls were "fussy and impractical", unlike the "sensible, practical, durable ranges designed for boys".
Recently, the Advertising Standards Authority introduced guidelines for gender stereotyping in ads.