Levonelle is available over-the-counter
The Society for the Protection of the Unborn Child (SPUC) had challenged the government's decision to allow the medication to be sold over-the-counter to over-16s.
But the High Court rejected SPUC's case following a judicial review.
SPUC now plans to seek leave to appeal against the court's decision.
It had claimed that emergency hormonal contraception is in fact a method of early abortion and, as such, should be subject to the abortion legislation.
SPUC's argument was based on the fact that the drug stops an embryo from implanting in the lining of the womb.
It also quoted the 1861 Offences Against the Person Act which prohibits the supply of any "poison or other noxious thing" with intent to cause miscarriage.
But the judge, Mr Justice James Munby, decided a woman was not legally pregnant before that stage and therefore the medication did not cause a miscarriage.
'Systematic deception'
He said a decision in SPUC's favour would also have affected other forms of contraception, such as IUDs (known as the coil) and the mini-pill.
He said: "In my judgement, the prescription, supply, administration or use of the morning-after pill does not - cannot - involve the commission of any offence under either 54 or section 59 of the 1861 Act."
He added there would be something "grievously wrong" if a 141 year-old law was held to mean possibly millions of people were, and had been, breaking the law.
If SPUC had been successful, the morning-after-pill would only have been available to women if prescribed by two doctors - the same restrictions which cover abortions.
Paul Tully, general secretary of SPUC said: "It is a sorry day for justice when the courts fail to protect unborn life at its most vulnerable.
"What the government, the drug company and the pro-abortion lobby have not been able to deny is that the early developing human embryo is killed by this drug."
He added: "We want to see today's judgement challenged in the Court of Appeal, and before the bar of public opinion."
'Vexatious attack'
Anne Weyman, chief executive of the Family Planning Association (FPA), which had opposed SPUC's action, said: "We are delighted that common sense has prevailed and this ridiculous action brought by the SPUC has been totally defeated."
She added: "This judicial review was a vexatious attack on women's reproductive rights and a dreadful waste of public and private time and money."
The British Medical Association's Head of Science and Ethics, Dr Vivienne Nathanson, said: "Emergency contraception can be taken up to three days after unprotected sex and it is therefore essential that access to it is made as easy as possible."
Availability
The morning-after-pill has been available from pharmacists to women over 16 from the beginning of last year.
Levonelle comprises two tablets of 750 micrograms of the a form of the hormone progestogen.
It can be taken up to 72 hours after intercourse.
It prevents unwanted pregnancy in several ways, depending on what stage of her menstrual cycle a woman is in when she has unprotected sex: