The Linda Norgrove Foundation will set up the scheme after receiving a grant of nearly £500,000 from the United States International Development Agency (USAID), specifically to fund the establishment of the libraries and literacy schemes for women and girls.
Some 840 women will receive literacy classes and more than 20,000 people are expected to use the community libraries being set up by Afghanistan Reads, a community literacy project supported by the Norgrove Foundation.
Literacy in Afghanistan is among the lowest in the world. It is estimated only 20% of women are literate and the figure is three times lower in rural areas.
Recent research from Unicef Afghanistan suggests only a third of women educated to primary school level retain their literacy skills because of a lack of ongoing access to written materials.
A pilot project, run by Canadian Women for Women in Afghanistan (CW4WAfghan) in partnership with the Norgrove Foundation, has already proved successful in tackling the problem.
Linda Norgrove grew up on Lewis, and was working in Afghanistan for the second time in 2010 when she was kidnapped. The 36-year-old was killed by a grenade thrown by a member of the US special forces in a failed rescue attempt.
Her parents, who still live on the island, set up the foundation in her name.
So far it has distributed £305,000 to projects and groups supporting women and children affected by the war in Afghanistan.
Linda's father John Norgrove welcomed the news of the $625,000 USAID grant. He said: "This is a project which can change so many lives. Education will empower women and is fundamental to the future of Afghanistan. It was a cause that Linda believed in passionately.
"This is a country that has seen so much turmoil and tragedy over the years but we believe that will only come to an end if the citizens, particularly women , are educated and empowered to change things for the better.
"We are a very small charity largely run by volunteers and do not have the capacity to run a project of this size. The opportunity to work with an established charity, with an established operation in Afghanistan, meant we could apply for support from USAID."
The Linda Norgrove Foundation has funded the literacy pilot project for some time and was impressed by the commitment and organisation of the members of the Canadian charity.
They realised what could be delivered if similar support was available on a wider scale.
The USAID grant will allow CW4WAfghan to run the community literacy project for two years. It is a huge boost in funds, but Mr Norgrove said donations were still needed to fund other important work.
"This is a generous sum, but it is ring-fenced and we will have to continue to find money for the other vital projects we support such as the Disabled Children's Home, the scholarships for women to study law and the medical treatments for children and women," he said.
CW4WAfghan executive director Janice Eisenhauer said she was very encouraged by the partnership with the foundation and the expanding relationship developing between the two community-based organisations.
She said: "It is an honour and a pleasure for our members in Canada and our Afghan staff in Kabul to have this opportunity to work in partnership with the Linda Norgrove Foundation. We share the same passion, commitment and goals towards universal human rights in Afghanistan and together we can strengthen our grassroots efforts."