The local authority was forced to seek out a court declaration that A had sufficient capacity to make the decision herself.
This was to ensure that doctors, medical staff, and hospital administrators could not be sued if they performed the procedure.
Mr Justice Mostyn was quoted in the Daily Mail noting that those under 16 are able to purchase contraception if they demonstrate "sufficient understanding and intelligence".
Justice Mostyn said that A had been interviewed by a consulting psychiatrist who had concluded that she had "a very clear understanding of her position and of the options that were available to her".
Christian Concern quoted the psychiatrist's description of A's state of mind and her reasons for seeking out an abortion: "She felt that she could not cope with its continuance and it would stress her to a considerable degree."
The psychiatrist had reportedly said that the choice was "hers alone and not the product of influence by adults in her family" and that he was therefore "completely satisfied" that she had the capacity to decide whether to have an abortion.
Members of the pro-life community has been angered by the decision. Andy Stephenson from Abort67 was quoted by Christian Concern saying: "This young girl is soon to be yet another victim of our twisted system that promotes sexual activity at an ever earlier age, followed by the tax funded death of any resulting 'mistakes'.
"I find it utterly abhorrent that she is being deceived by those who should be protecting her and her child. It is complete nonsense that a court can rule that she is competent to make such a decision when the facts about abortion are systematically hidden from her by those who provide abortion, schools and tragically many pro-life groups.
Data from the Office for National Statistics show that 5,432 under-16s fell pregnant in 2012, down 9 per cent on the year before, but still higher than France, Germany, and Japan.
The National Institute for Clinical Excellence has recommended that free condoms be made available in youth clubs, sixth form colleges, and schools, to cut teenage pregnancy rates.
Although minors need parental permission for some medical treatments, contraceptive implants and injections can be provided to children without parental consent because of doctor-patient confidentiality rules.
The 2010-2011 NHS figures reveal approximately 3,200 girls aged 15 were fitted with contraceptive implants, and 1,700 had injections.
The data also shows that 1,700 girls aged 13 and 14 were fitted with contraceptive implants in 2010-2011, while 800 had injections.