The country has become increasingly hostile to Southern Sudanese, who are largely Christian, since South Sudan gained independence in 2011.
The expansion of the Exodus campaign has been made possible by the generosity of donations from supporters but Barnabas Fund said it still needs another £76,000 to cover the full costs of the rescue.
The organisation, which supports persecuted Christians, has airlifted and bussed nearly 5,000 vulnerable Christians to South Sudan.
It says Christians in the overwhelmingly Muslim Sudan are facing oppression and hostility under an increasingly aggressive Islamist government that wants to eradicate the Christian presence from the North.
Around two thirds of the Christians rescued so far have been widows and children, and they will remain a priority in the next evacuation.
The Christians to be evacuated next have been living in tents on the edge of Khartoum for years, the organisation says.
They will be evacuated in partnership with Africa Inland Mission Sudan.
Suzy, a young mother who has been returned home, said, "After many years of suffering and prayers, God opened the way for us."
Dr Patrick Sookhdeo, International Director of Barnabas Fund, said: "We are very grateful that our supporters have been moved by the plight of their Christian family in Sudan to give generously to this rescue mission. We must now call on your help again as we prepare to assist more endangered women and children. Perhaps you could ask your church to have a collection for this cause?"