The visit is aimed at showing solidarity with the abducted schoolgirls and their families, Xinhua reported.
Mlambo-Ngcuka's visit came at a time when the education system in Nigeria falters amid fears of possible attacks on schools by Boko Haram, an Islamist group seeking to enshrine the Islamic Sharia law in the constitution.
During a visit to a girls' college in a Nigerian town of Abaji, Mlambo-Ngcuka assured that the UN would work together to ensure that there is no setback for girls' education in Nigeria, said Stephane Dujarric at a regular briefing.
About 270 girls from Chibok community in Nigeria's Borno State were abducted in April by Islamist group Boko Haram, who threatened to sell the girls in a video.
Specialist teams from several countries are searching for the girls, but scant progress has been scored so far.
"We are going to be here and we will work with you to ensure that when the girls return they are consoled, and with their families they get the support they need. The girls of Nigeria deserve the best education and the best care and support," Mlambo- Ngcuka said.