The Christians are being evacuated because of increasing hostility in the majority-Muslim country.
After South Sudan gained independence in 2011, the largely Christian Southerners living in Sudan lost their citizenship rights and were ordered to leave.
There is little sign of conditions improving as Sudanese President Omar al-Bashir has vowed to bring in a fully Islamic constitution and strengthen sharia law.
The Christians in the Barnabas evacuation programme are being taken to South Sudan, which is largely Christian.
The evacuees, who include women and children, are being transported by bus in partnership with Africa Inland Church Sudan.
There are plans to rescue another 1,500 from Sudan.
Dr Patrick Sookhdeo, International Director of Barnabas Fund, said: "It has been wonderful to see the Lord's hand at work in the Exodus mission.
"There have been many difficulties and setbacks, but each time He has opened the way and has made this endeavour more fruitful than we could have asked or imagined.
"We pray that He will continue to bless this work so that many more Christian women and children trapped in Sudan can be helped to safety."