The government hopes that the studying time lost by the country's 1.8 million children can still be made up.
The United Nations Children's Fund (Unicef) says that the reopening of Sierra Leone's schools marks "a major step in the normalisation of life".
New cases of Ebola continue to be reported in Sierra Leone but numbers are declining.
The BBC's Umaru Fofana reports from the capital Freetown that the pupils are "really excited" to be going back despite concerns about Ebola.
To allay fears and ensure that there are no new Ebola cases, the first day at school will be spent on Ebola education and going through basic hygiene rules.
Unicef has trained 9,000 teachers in Ebola prevention and is also supplying hand washing facilities to every school.
There will also be the chance to remember friends and colleagues who died from Ebola.
Secondary school teacher Nancy Banya told the BBC's Newsday programme that after welcoming the children there will be a quiet time to reflect on the lives of "those friends who we lost".
There have been more than 12,000 Ebola cases in Sierra Leone with 3,831 people dying from the virus since the outbreak began in the country in May 2014, according to the World Health Organization.
The number of new cases is declining with just six recorded last week.
At the start of the school day pupils will be required to wash their hands with soap and clean water and have their body temperature checked before entering the classroom, our reporter says.
But he adds that there is concern that school facilities will not be ready.
He visited several schools in different parts of the country where the classroom furniture was broken and the compounds were covered in overgrown grass.
Despite this many pupils will be pleased, says Ms Banya, as the "kids are so bored" staying at home.
Sierra Leone is the last of the three countries worst affected by the Ebola virus to reopen schools. Guinea reopened its schools in January and Liberia followed a month later.
Schools have reopened across Sierra Leone nine months after they were closed because of the Ebola outbreak.