The Medicines and Healthcare products Regulatory Agency (MHRA) in UK said there was a small risk of severe allergic reactions and this outweighed any perceived benefits.
Some people take the tablets to reduce the severity of cold and flu.
The MHRA said it was a precautionary measure and older children and adults could continue to use echinacea.
It said young children were at heightened risk of allergic reactions such as rashes, hives, difficulty in breathing and even potentially fatal anaphylactic shock.
Richard Woodfield, the head of herbal policy at the MHRA, said: “This is not a serious safety issue, but parents and carers need to be aware that children under 12 could have a low risk of developing allergic reactions.
“The measures being taken are precautionary in nature. Parents should not worry if they have given echinacea to children under 12 in the past.”
Licensed products containing echinacea, some of which are aimed at children, will have to be labelled with the warning.
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