With people still living in classrooms at some schools, arrangements had to be made for students at those institutions to study elsewhere.
Authorities needed "more time to prepare the schools that are occupied by displaced families," education ministry spokeswoman Salama al-Hassan said, meaning classes could not begin as scheduled on September 21 in areas controlled by the federal government.
In the autonomous Kurdish region in the north, which has a separate educational system, classes started last month.
An estimated 1.8 million people have been displaced by violence since the beginning of the year.
Insurgents seized all of one city and parts of another west of Baghdad in January, sparking the first round of displacements.
Hundreds of thousands more fled their homes after militants led by the Islamic State (IS) group launched a sweeping offensive in June.
A building that holds two primary schools in the Saidiyah area of southern Baghdad is currently housing more than 30 families, two to a room.
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Students and their parents visited the school Wednesday to pick up books and other supplies before heading to another school where they will attend class for three hours a day.
"The displaced are our responsibility, but we blame the state. It must give them their rights and our rights," said Bushra Abdulhur Kadhim, the principle of the Umm Qasr school.
Other students were luckier Wednesday.
At a primary school for girls on Palestine Street in central Baghdad, students dressed in blue and white uniforms arrived with their parents amid tight security.
The school administration held a celebration to mark the opening day, raising the flag and playing the national anthem over speakers.
But for students still in large areas north and west of Baghdad that are outside government control, the situation is far more dire.
"Students in... any area not controlled by the government will receive lessons via educational television," with an exam at the end of the year, Hassan said.