Correspondents said the atmosphere at schools was subdued and many pupils had not returned.
They said parents had been taken by surprise by the government's decision to reopen schools with only four days' notice and many were not prepared.
More than 8,400 people have died in West Africa in the world's worst outbreak of the Ebola virus.
The reopening of schools in Guinea comes four days after the UN said the number of confirmed Ebola cases in the country had fallen to its lowest weekly total since August.
At one school in the Guinean capital, Conakry, only about 220 of the approximately 2,000 pupils were reported to have returned.
Of the 36 teachers, more than half were back at work.
Many schools have introduced health precautions, including hand-washing and temperature checks.
Ebola has had a severe impact not only on public health but also on the Guinean economy.
Unemployment and underemployment have risen, leaving many parents with difficulties meeting school-related expenses at the beginning of a new academic year.
Schools remain closed in Sierra Leone and Liberia, the two other countries hit hard by the Ebola outbreak.
Earlier this month, the outgoing head of the UN team fighting Ebola, Anthony Banbury, said he believed cases of the virus would be brought down to zero by the end of 2015.
Schools have been reopening in Guinea after a five-month closure because of the deadly Ebola outbreak.