The project has the support of aid from the Department for International Development after the charity won its bid for funding under the UK Government's Global Poverty Action Fund programme.
The million pound project got underway in April and will run for three years, bolstering the health work that the charity has undertaken in the country since 2006.
The project will focus primarily on providing essential maternal child health services in the Napak district of Karamoja, which has one of the highest maternal mortality rates in Uganda.
One in five children die before they reach their fifth birthday in this district, a much higher rate than the rest of the country, which is one in ten.
Funds will also be used to provide services aimed at improving the health of mothers and pregnant women by resourcing them with information and skills.
Samaritan's Purse aims to establish 200 care groups and reach an estimated 32,000 pregnant women and caregivers of children under five.
It is hoped that men will also come on board to help women improve their maternal health.
"The main thing is that the health of mothers and pregnant women will improve and more children under five will survive," said Samaritan's Purse executive director, Simon Barrington.
"They'll no longer suffer from malaria, cholera, dysentery and diarrhoea, but actually their mothers will be helped to look after them. They will be helped to grow and develop into healthy young human beings and have a secure future."
Mr Barrington has just returned from Uganda where he saw the impact of the project in Karamoja first hand.
He visited several health clinics and found that health workers did not have the resources to get out to the rural communities there.
Mr Barrington said the project would establish "lead mothers" across 2,000 communities who will provide additional support to the health workers by offering ante natal and post natal care for local children.
"This is a tremendous partnership between the local government in Karamoja, Samaritan's Purse and the UK government," he continued.
"This support from the Department for International Development is a real recognition of the excellent work that people have seen us doing in the field, the quality of the work and also the effectiveness of it as well.
"We really appreciate this support from the British Government partnering with us to make sure this programme works well and is effective for giving healthy lives and a future for these children and their mothers."