Hundreds of Nigerians travel to the US each year for education, jobs and healthcare.
In announcing the retaliatory action, the US authorities disclosed that Nigeria charges US citizens higher fees for visas than Nigerians pay for US ones.
The price for a US citizen to get a Nigerian visa is currently $180 (£146).
The new levies for Nigerians range from $80 to $110 and will only apply to those whose visa applications have been approved.
The decision comes after consultations with the Nigerian government to reduce its visa fees for US citizens failed to yield results.
The new fee takes effect from Thursday 29 August.