It's issued new guidance for professionals when their religion, personal values or beliefs might impact on their willingness to provide certain services.
There had been some concern over the guidelines. Some suggested they were bringing about a change which would take away a pharmacist's right to refer patients to another professional.
Campaign group the Christian Institute said it was willing to take legal action to prevent the change claiming it went against laws which protect freedom of thought, conscience and religion.
Unveiling the new document, the GPhC said: "The new guidance incorporates feedback heard through the consultation process.
"For example, we heard from respondents to the consultation that the guidance would be relevant to a wide range of situations, and not just those involving emergency hormonal contraception.
"The guidance is also clear that referral is still an option, but may not always be enough; for example, if a service is not accessible or available elsewhere or, if due to the person's vulnerability, a referral would effectively obstruct timely access to the service."
Duncan Rudkin, Chief Executive of the GPhC, said: "We recognise and respect that a pharmacy professional's religion, personal values and beliefs are often central to their lives and can make a positive contribution to their providing safe and effective care to a diverse population.
"This guidance is intended to reflect the broad range of situations when a pharmacy professional's religion, personal values or beliefs might impact on their willingness to provide certain services. It will support pharmacy professionals to make good decisions and provide person-centred care, within the legal framework.
"We would encourage all pharmacy professionals and owners to be familiar with this guidance and, where necessary seek further independent advice and support."
The guidance has been welcomed by the Christian Institute.
In a statement, Solicitor Advocate Sam Webster, who heads up The Christian Institute's Legal Defence Fund said: "This is a relief for pharmacists. It simply shows a bit of respect for people of faith and by doing so should more or less maintain the status quo in practice for pharmacists and their customers.
"We're grateful to the GPhC for offering to meet with us earlier this year to discuss our concerns. However, we were fully prepared to litigate and made this clear in pre-action legal correspondence exchanged with the Council's lawyers.
"We reminded them of the obligations of human rights law, which protects the right to freedom of thought, conscience and religion.
"There's no doubt the new guidance reflects key points that we argued with the Council and we are pleased that they have taken those arguments on board."