The decision to resume classes next Monday was reached at a cabinet meeting.
Schools and the universities in Benin have been shutdown since March 30, as part of a series of measures taken by the authorities to curb the spread of Covid-19.
CM2, middle and high school students are those mainly targeted by the resumption which comes into effect on May 11.
Students will follow online courses via a platform, because the amphitheaters will remain closed.
A platform with free access to students has been set up for teachers to publish their lessons, local online news outlets said, quoting the cabinet.
For schoolchildren from CI to CM1, their return to school is scheduled from August 10 to September 4 and their assessments will be made from September 7 to 11.
Kindergartens and daycare centres will remain closed until September 28.
The mandatory wearing of a mask for all users and the systematic and gradual screening of teachers, as well as administrative and service staff are among the measures to be observed before resumption.
In addition, the council decided to lift the health cordon which isolates certain cities at risk to prevent the spread of the virus across the country.
As of May 11, all checkpoints around the 16 cities isolated since March 30 will be lifted.
Beninese will therefore be able to go everywhere without the need for an exemption by a prefect, although barrier measures will remain in force.
Benin has so far declared 96 Covid-19 cases, including 50 recoveries and two deaths.