The chain faced criticism after refusing to reduce the cost of the morning-after pill over fears it could incentivise its use.
Labour MPs attacked the company for taking an “unacceptable” moral position and health campaigners claimed women were being hit with a “sexist surcharge”.
A spokesman for Boots said: “Pharmacy and care for customers are at the heart of everything we do and as such we are truly sorry that our poor choice of words in describing our position on emergency hormonal contraception (EHC) has caused offence and misunderstanding, and we sincerely apologise.”
Boots charges £28.25 for Levonelle emergency contraceptive and £26.75 for its own version, while Tesco charges £13.50 for Levonelle and Superdrug £13.49 for a generic product.
The British Pregnancy Advisory Service (BPAS), which launched the campaign calling on Boots to reduce the price tag on the emergency contraceptive, found the progestogen-based pills can cost up to five times more in the UK than other parts of Europe.
Boots said its price tag was based on the cost of the medicine and the consultation the pharmacists carries out with women but it is “committed” to finding less expensive versions of the tablet.
It said: “We firmly believe in the right of all women to access the EHC service with ease and convenience, and have long been at the forefront of increasing accessibility of contraception for women.
“The provision of EHC requires a regulated mandatory consultation to protect women’s health and is a professional healthcare service provided by highly trained pharmacists. As a leading pharmacy, we will not compromise or undervalue this professional service.
“The consultation with the pharmacist is necessary to understand the patient’s individual circumstances and ensure we provide an appropriate, safe and effective medicine for her.
“The pricing of EHC is determined by the cost of the medicine and the cost of the pharmacy consultation. We are committed to looking at the sourcing of less expensive EHC medicines, for example generics, to enable us to continue to make a privately funded EHC service even more accessible in the future.
“In addition the NHS EHC service where it is locally commissioned, is provided for free in over 1,700 of our pharmacies, and we continue to urge the NHS to extend this free service more widely.”
It comes after a letter organised by Labour’s Jess Phillips and backed by the party’s women MPs expressed “deep concern” about the position Boots had taken and called for the chain to follow its rivals in cutting the cost.
The letter said: “The justification given by Boots for maintaining the high price was that it did not want to face complaints or to incentive the use of emergency contraceptive.
“This infantilises women, Boots largest customer base, and suggests Boots takes a moral position against women’s choice which is unacceptable.”
It added: “The women of the PLP (Parliamentary Labour Party) implore you to commit to following the example set by Superdrug and Tesco and agree to reduce the cost of emergency contraception at Boots.
“It will improve women’s access to a vital method of back-up contraception, is supported by the majority of the public, is clearly commercially possible and will end the sexist sub-charge on emergency contraception.”
BPAS welcomed the apology and said it was “delighted”.
Clare Murphy, director of external affairs said: “We really welcome this apology from Boots and are delighted that they are committed to lowering the cost of emergency contraception.
“We look forward to learning what the next steps will be and the time-frame for these changes.
“As other retailers have been able to introduce a price reduction across their stores we hope Boots will act promptly to ensure women have affordable access to this back-up method of contraception, which gives women a crucial second chance of avoiding an unwanted pregnancy.”