The attack took place on Tuesday at a school attached to the privately-run Ateneo de Zamboanga University in the city of Zamboanga.
The gunman brought a pistol and a rifle onto the school campus and fired at students inside the classroom, according to a preliminary police report.
The gunman, a grade 9 student, took his own life. The victim was a male student a grade above him, police said.
The university's president Ernald Andal confirmed there were no additional fatalities or reported injuries.
"We do not want any of these things to happen. We wish to prioritise the safety of all our students," Andal said.
The shooting followed an attack in June at a public high school in Tacloban City in which at least three students were killed and about 20 others injured when two of their schoolmates opened fire on campus.
School shootings are rare in the Philippines, which has relatively strict gun ownership regulations, including background checks and psychological evaluation requirements, although illegal firearms remain in circulation.
News channel ANC showed footage of students and parents gathering outside the school gates with some armed police and soldiers present. Crime scene investigators were seen arriving at the school.
The school is a five-storey building on 20-acre site that houses the university's grade school and junior high school students, according to its website.
The incident came less than 10 days after a high-profile incident in Thailand, where a student went on a shooting rampage at a school on the outskirts of the capital Bangkok.
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