Alphonse Laveran was born at Boulevard Saint-Michel in Paris, to parents Louis Théodore Laveran and Marie-Louise Anselme Guénard de la Tour Laveran. He was an only son with one sister. His family was in a military environment. His father was an army Doctor and a Professor of military Medicine at the École de Val-de-Grâce. His mother was the daughter of an army commander. At a young age his family went to Algeria to accompany his father's Service. He was educated in Paris, and completed his higher education from Collège Saint Barbe and later from the Lycée Louis-le-Grand. Following his father he chose military Medicine and entered the Public Health School at Strasbourg in 1863. In 1866 he became a resident medical student in the Strasbourg civil hospitals. In 1867 he submitted a thesis on the regeneration of nerves and earned his medical degree from the University of Strasbourg.

At the outbreak of the Franco-Prussian War in 1870, he joined the French Army. At the age of 29 he became Chair of Military Diseases and Epidemics at the École de Val-de-Grâce. At the end of his tenure in 1878 he worked in Algeria, where he made his major achievements. He discovered that the protozoan parasite Plasmodium was responsible for malaria, and that Trypanosoma caused trypanosomiasis or African sleeping sickness. In 1894 he returned to France to serve in various military health services. In 1896 he joined Pasteur Institute as Chief of the Honorary Service, from where he received the Nobel Prize. He donated half of his Nobel money to establish Laboratory of Tropical Medicine at the Pasteur Institute. In 1908 he founded the Société de Pathologie Exotique.

Laveran was Medical Assistant-Major of the French Army at the time of Franco-Prussian War. He was posted to Metz, where the French were eventually defeated and the place occupied by Germans. He was sent to work at Lille hospital and then to the St Martin Hospital (now St Martin's House) in Paris. In 1874 he qualified a competitive examination by which he was appointed to the Chair of Military Diseases and Epidemics at the École de Val-de-Grâce, a position his father had occupied. His tenure ended in 1878 and he was sent to Algeria, where he remained until 1883. From 1884 to 1889 he was Professor of Military Hygiene at the École de Val-de-Grâce. In 1894 he was appointed Chief Medical Officer of the military hospital at Lille and then Director of Health Services of the 11th Army Corps at Nantes. By then he was promoted to the rank of Principal Medical Officer of the First Class. In 1896 he entered the Pasteur Institute as Chief of the Honorary Service to pursue a full-time research on tropical diseases.

In 1880, while working in the military hospital in Constantine, Algeria, he discovered that the cause of malaria is a protozoan, after observing the parasites in a blood smear taken from a patient who had just died of malaria. He found the causative organism to be a protozoan which he named Oscillaria malariae, but later renamed Plasmodium. This was the first time that protozoans were shown to be a cause of disease of any kind. The discovery was therefore a validation of the germ theory of diseases.

Laveran married Sophie Marie Pidancet in 1885. They had no children.

Laveran was awarded the Bréant Prize (Prix Bréant) of the French Academy of Sciences in 1889 and the Edward Jenner Medal of the Royal Society of Medicine in 1902 for his discovery of the malarial parasite. He received the Nobel Prize in Physiology or Medicine in 1907. He gave half the Prize for foundation of the Laboratory of Tropical Medicine at the Pasteur Institute. In 1908 he founded the Société de pathologie exotique, over which he presided for 12 years. He was elected to membership in the French Academy of Sciences in 1893, and was conferred Commander of the National Order of the Legion of Honour in 1912. He was Honorary Director of the Pasteur Institute in 1915 on his 70th birthday. He was elected President of the French Academy of Medicine in 1920. His work was commemorated philatelically on a stamp issued by Algeria in 1954.

Laveran was elected to French Academy of Sciences in 1893, and was conferred Commander of the National Order of the Legion of Honour in 1912.

In 1922 he suffered from an undefined illness for some months and died in Paris. He is interred in the Cimetière du Montparnasse in Paris. He was an atheist.

Laveran's name features on the Frieze of the London School of Hygiene & Tropical Medicine. Twenty-three names of public health and tropical Medicine pioneers were chosen to feature on the School building in Keppel Street when it was constructed in 1926.