Demonstrators clashed with police in the capital Niamey as they showed their anger at the French magazine Charlie Hebdo.
The newspaper published the cartoon a week after an Islamist terror attack at its Paris offices.
Amadou Abdoul Ouahab, who took part in the demonstration, told Reuters: "They offended our Prophet Mohammad, that's what we didn't like.
"This is the reason why we have asked Muslims to come, so that we can explain this to them, but the state refused. That's why we're angry today."
Police fired tear gas at the gangs who were throwing petrol bombs and stones in retaliation, some held posters saying they were 'Kouchi', in reference to the name of one of the Paris attackers.
The protests had been banned by the government.
On Friday churches and Christians shops and homes were burnt in Niger's second city, Zinder.
Emergency services have revised the death toll from that protest to five after finding a body inside a burnt out church.
Protests have also been held in smaller towns where churches have also become targets.
Elsewhere peaceful demonstrations took place in Mali, Senegal, Mauritania, Algeria and Pakistan.