Irn-Bru to carry a health warning
AG Barr was asked more than two years ago to remove the yellow and red colourings after a study found a link between seven key additives and children's behaviour.
A new European Union law means Irn-Bru and Lucozade Original must display warnings that the additives "may have effects on activity and attention in children".
However, shops can sell stock produced before the law came in last week.
Irn-Bru is the most lucrative product for Barr's, which saw its pre-tax profits soar last year to a healthy 27.9 million.
Lucozade Original contains sunset yellow, which is also in the recipe for Irn-Bru, along with a red colouring, ponceau.
An FSA study published in 2007 officially recognised a link between six artificial colourants and children's behaviour and urged a voluntary ban on them. Although Barr and Lucozade manufacturer, Glaxo-SmithKline, have agreed to remove the additives, they are still working to ensure their products retain their distinctive colours.
Tests found children who consumed the additives had a small reduction in attention span, with some becoming significantly more hyperactive.
An FSA spokesman said: "The mandatory warning will make it easier for people to choose products free from these colours."
However Jackie Schneider, co-ordinator of the Children's Food Campaign, said: "It's completely irresponsible.
"We would rather they didn't use them, but if they do, they should be clearly labelled."
A spokeswoman for AG Barr said: "We are fully committed to replacing two food colours in our products in line with FSA guidelines.".
A spokesman for Glaxo-SmithKline added: "We are committed to finding an alternative to sunset yellow and have invested significantly in exploring viable alternative formulations."