The son of a military surgeon, Lavaran was born in Paris and studied medicine at the University of Strasbourg, obtaining his MD in 1867. Like his father, he joined the Army Medical Service and served in Algeria (1878–83).

In 1880 Laveran made one of the most important discoveries of 19th-century medicine, namely, the causative agent of malaria. In Algeria he frequently performed autopsies on malaria victims who, he noted, had numerous pigmented bodies in their blood. Although some of these bodies were in the red blood cells he also noted other free bodies, at the edge of which he observed moveable filaments or flagella. The extremely rapid and varied movements of these flagella indicated to Laveran that they must be parasites. He found such parasites in 148 out of 192 cases and thus assumed them to be the cause of malaria. He called the parasite Oscillaria malariae but the Italian name Plasmodium later won favor.

Laveran also speculated that mosquitoes might play a part in transmitting malaria but he failed to follow up this insight. In 1883 he returned to France to become professor of military hygiene and parasitology at the Val-de-Grace School of Military Medicine and in 1897 moved to the Pasteur Institute where he remained until his death. Here he published important works on leishmaniasis and trypanosomiasis.

In 1884 Laveran published Traité des fièvres palustres (Treatise on marsh Fevers), which later won him the 1907 Nobel Prize for physiology or medicine for showing the role played by protozoa in causing disease. With the prize money he founded a laboratory of tropical medicine at the Pasteur Institute.