But the father will shoulder the cost of doing so.
The mother had sought in a injunction in the Family Court to stop the father and his partner from immunising the child without her written permission.
She made the application after discovering that her daughter's stepmother had secretly taken the child to a medical centre to have her immunised against diphtheria, tetanus, pertussis, hepatitis B, polio, HIB, measles, mumps, rubella and meningococcal C.
Previously, the mother had been arranging homeopathic vaccines.
She told the court that she adhered to a ''simple and healthy way of life'', that included eating organic food, using non-toxic cleaning products and sending the child to a Rudolph Steiner school where the toys were made from natural products such as wool, wax and silk.
Most parents at the school focused on ''building up the immune system of the child through homeopathics'', she told the court.
But when the girl was five, she contracted whooping cough, and the father and his new partner became concerned that she was not vaccinated, possibly placing their new baby at risk.