The government's Medicines and Healthcare products Regulatory Agency (MHRA) said there was no "robust evidence" that many popular products worked, while side effects included sleeping difficulties, allergic reactions and even hallucinations.
Clinical trials have traditionally not been required to demonstrate that products work specifically in children. The agency said this thinking was changing.
"It is not right to assume safety and efficacy based on children being small adults," said June Raine, MHRA's director of vigilance and risk management. "Children should have access to medicines that are acceptably safe and designed for their use."
High street pharmacy Boots said it would be following the advice, while the trade body for medicine manufacturers, the Proprietary Association of Great Britain, said the affected remedies would no longer be marketed for youngsters.
For children under six, the government's watchdog recommends parents stick to remedies to lower a child's temperature and simple honey and lemon mixtures to ease a cough. Still, it said parents should not worry about previous medicine use and said shop shelves did not need to be cleared of current stocks.
Do you think most over-the-counter medicine is safe to use on children?