The teacher had recently discussed caricatures of the Prophet Mohammed in class, according to police and media sources.
France’s anti-terror prosecutor said it was investigating the attack, which took place in Conflans-Sainte-Honorine, a suburb north-west of Paris, at around 5:00 pm (1500 GMT) on Friday.
Macron headed to the scene following an emergency meeting at the French interior ministry.
Decrying an “Islamist terrorist attack”, the French president said the whole country stood united behind its teachers.
“A citizen has been murdered today because he was a teacher and because he taught freedom of expression,” Macron said near the school where the teacher was killed.
“Terrorists will not divide France, obscurantism will not prevail,” Macron added.