The lead poisoning crisis in northwest Zamfara state that first came to light in 2010 was "the worst outbreak ever recorded," MSF said, with an official death toll saying 400 children were killed across the state.
Before it could treat the children, medical workers first needed to clear affected areas of the toxins through a process called remediation.
The promised $3 million (2.3 million euros) for remediation met with repeated delays and the government of Nigeria, Africa's largest oil producer, faced mounting pressure from activists saying more children were unnecessarily put at risk.
Most of the funds were released in late January and on Tuesday MSF announced that remediation had been completed in some areas.
"MSF is very happy to have finally -- after three years -- begun medical treatment in Bagega," the most acutely affected area in Zamfara, a statement said.
But thousands of children remain at risk, the medical aid group said, because remediation remains unfinished in some areas and the work must stop when the rains become too heavy, which could happen any week.
"Our teams are under tremendous pressure to finish the remediation on a very tight schedule," said Simba Tirima of the TerraGraphics Foundation which is overseeing the operation.
Lead was dispersed in several Zamfara areas by the processing of ore for gold extraction using unsafe mining techniques. Illicit gold mining is more lucrative than agriculture for the impoverished farming communities.
Local communities had initially largely concealed or denied the fatalities and illnesses from lead poisoning for fear that authorities would ban their mining activities.