MSF (Doctors Without Borders) said it took the decision to pull out after its request to be allowed to resume its work received no response.
MSF was conducting nutritional programmes in the south central region of Maradi.
In July the government in Niamey suspended MSF on the grounds that it was refusing to work with public services and was guilty of the "endemic malnutrition" of children.
"As we have not received a response from Niger authorities and in view of government statements, the French section of Medecins sans Frontieres cannot help but leave the country," MSF said in a statement sent to AFP.
A leading trade union body had called earlier Wednesday for the ban to be lifted.
"This seemingly fallacious measure has unbearable social consequences for a country as poor as Niger," the federation of workers' unions in Niger said in a statement.
These included the "worsening of the situation of several thousand malnourished children" and the loss of more than 500 jobs of locally-employed staff.
MSF said its "departure provides an occasion to stress once again the need to immediately attend to the malnourished children in Maradi, to recall that it is urgent - at an international level - to recognise malnutrition as a public health priority."
It recently indicated that since it was suspended three months ago, "nearly 8,000 children" were suffering from severe malnutrition in two central districts of Madarounfa and Guidan Roumdji, in Maradi, the most affected region of the vast and arid west African nation.
Niger's health minister Issa Lamine last week rallied parliamentarians against the charity.
"Let MSF leave and let the state be able to deploy the means needed to take charge of the people's health."
Lamine charged MSF with providing "false" statistics about children suffering from malnutrition in order to "mobilise a lot of money" from donors and said "the situation is not dramatic at Maradi".
Earlier this month, MSF-France earlier this month sent its president Marie-Pierre Allie to Niamey in an effort to resolve the problem.
President of MSF international, Christophe Fournier, is due to hold a news conference Thursday in Niamey.
Niger is ranked one of the most impoverished countries on earth, sitting just four places from the bottom of the UN poverty indicator list of 177 nations.