Violence broke out at the Baptist Secondary School in Ilorin, the Kwara State capital, on Wednesday following a clash between Muslim and Christian protesters over the use of hijabs.
Eyewitnesses say Christian parents at the school barred female Muslim students from entering the school on Wednesday.
This led to a clash with their Muslim counterparts, which later escalated to the rival groups throwing stones and plastic chairs at each other.
Police also fired tear gas after some Muslim protesters tried to pull down the school sign-board.
The Baptist Secondary School was one of the 10 shut down last month by the state government over the controversy and reopened only on Wednesday.
The state government had waded in and ordered the closure of the schools to avert violent clashes by Christian and Muslim groups.
On Tuesday, it announced that the schools had been told to reopen to enable students to prepare for the West African Senior School Certificate Examination but warned that the schools must respect its policy that allows the use of the hijab in all public schools.
The schools were set up by Christian missionaries many years ago, but the military government, in the 1970s, took over these schools from the missions.
The missions in Kwara had twice challenged the government take-over of the schools in court but lost the suit at the high court and appellate court.
The missions, comprising different Christian denominations, have taken the case to the Supreme Court.