The British Pregnancy Advisory Service (BPAS) has been lobbying to change the law in the UK and welcomed the development.
The abortion pill can be taken for pregnancies under nine weeks gestation.
The medical abortion involves taking two different medicines which are administered separately, they can be taken at the same time or three days apart.
The effectiveness of the medication is lessened if the pills are taken at the same time, despite it being more convenient.
Under the changes, women in Scotland will have to go to a clinic for the first pill, but can now take the second stage of medication home to be administered rather than return again.
Ann Furedi, chief executive of BPAS, said: “We thoroughly welcome the Scottish government’s decision.
“This will spare women not only the difficulties associated with having to make more than one clinic visit, childcare, transport, time off work, but it will also spare women from the risk of symptoms on their way home, having taken the medication in a clinic.
“It is simply perverse that a woman arriving at a BPAS clinic in England and Wales with an incomplete miscarriage can be given the medication to take in the comfort and privacy of her own home, while a woman seeking an abortion must take that same medication on site.
“We hope that the government will follow Scotland’s lead and roll out this important policy change across the rest of Great Britain.”
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Campaign groups, including Engender, Amnesty Scotland and Rape Crisis Scotland had said making women travel to clinics to take the pill “denies women clear potential advantages in terms of their wellbeing at what is often a very difficult time”.
The Scottish Government said the move did not require a change in the law but came under existing powers available within the 1967 Abortion Act.
Scotland’s Public Health Minister Aileen Campbell said: “Abortion can be an emotive subject, however I am proud this government is working hard to ensure women are always able to access clinically safe services.
“Scotland is now the only part of the UK to offer women the opportunity to take misoprostol at home when this is clinically appropriate, a decision that allows women to be in control of their treatment and as comfortable as possible during this procedure.”
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