At least 1,000 young people assembled at the grand mosque in the capital Niamey, some of them throwing rocks at police.
The protests erupted after French satirical magazine Charlie Hebdo published more cartoon images of the Prophet Mohammad.
The demonstrators set French flags ablaze and attacked Christian shops with clubs and Molotov cocktails. Police responded with tear gas.
#BREAKING: At least two churches burned in Niger as Charlie Hebdo protests rage on: AFP— Agence France-Presse (@AFP) January 17, 2015
"The protesters were crying out in the local Hausa language: 'Charlie is Satan — let hell engulf those supporting Charlie'," Reuters quoted one of the witnesses, shopkeeper Aboubacar Mamane as saying.
Protests also erupted in Pakistan and Algeria, resulting in several injuries.
Peaceful marches took place after Friday prayers in the capital cities of several former French colonies in western Africa: Mali, Senegal and Mauritania.