Mechnikov was born in a village near Kharkov, Russian Empire, the youngest son of Ilya Mechnikov, a Guard officer, and Emilia Mechnikova (née Nevakhovich). His maternal grandfather Lev Nevakhovich was the first Russo - Jewish writer and founder of the Haskala movement in Russia. The family name Mechnikov is a translation from Romanian, since his father was a descendant of the Chancellor Yuri Stefanovich, the grandson of Nicolae Milescu. The word "mech" is a Russian translation of the Romanian "spadă" (sword), which originated with Spătar. His elder brother Lev became a prominent geographer and sociologist. Mechnikov was raised predominantly by his Jewish mother, and developed a passion for natural history. When Charles Darwin's The Origin of Species was published, Ilya vehemently undertook the survival of the fittest, testing and teaching it.

He attended Kharkov University where he studied natural sciences, completing his four-year degree in two years. He then went to Germany to study marine fauna on the small North Sea island of Heligoland and then at the University of Giessen, University of Göttingen and then at Munich Academy. In 1867 he returned to Russia to the appointment of docent at the new Odessa University, followed by an appointment at the University of St. Petersburg. In 1870 he returned to Odessa to take up the appointment of Titular Professor of Zoology and Comparative Anatomy.

Mechnikov became interested in the study of microbes, and especially the immune system. In 1882 he resigned his position at Odessa University and set up a private laboratory at Messina to study comparative embryology, where he discovered phagocytosis after experimenting on the larvae of starfish. He realised that the process of digestion in micro-organisms was essentially the same as that carried out by white blood cells. His theory, that certain white blood cells could engulf and destroy harmful bodies such as bacteria, met with scepticism from leading specialists including Louis Pasteur, Behring and others. At the time most bacteriologists believed that white blood cells ingested pathogens and then spread them further through the body.

Mechnikov returned to Odessa as director of an institute set up to carry out Pasteur's vaccine against rabies, but due to some difficulties left in 1888 and went to Paris to seek Pasteur's advice. Pasteur gave him an appointment at the Pasteur Institute, where he remained for the rest of his life.

Mechnikov's work on phagocytes won him the Nobel Prize in 1908. He worked with Émile Roux on calomel, an ointment to prevent people from contracting syphilis, a sexually transmitted disease.

Mechnikov also developed a theory that aging is caused by toxic bacteria in the gut and that lactic acid could prolong life. Based on this theory, he drank sour milk every day. He wrote three books: Immunity in Infectious Diseases, The Nature of Man, and The Prolongation of Life: Optimistic Studies, the last of which, along with Metchnikoff's studies into the potential life lengthening properties of lactic acid bacteria (Lactobacillus delbrueckii subsp. bulgaricus), inspired Japanese scientist Minoru Shirota to begin investigating the causal relationship between bacteria and good intestinal health, which eventually led to the worldwide marketing of Kefir and other fermented milk drinks, or probiotics.

Mechnikov was married to his first wife Ludmila Feodorovitch in 1863. She died from tuberculosis on 20 April 1873. Her death, combined with other problems, caused Mechnikov to unsuccessfully attempt suicide, taking a large dose of opium. He married again in 1875, to Olga Belokopytova who died in 1944 in Paris from typhoid. Mechnikov died in 1916 in Paris from heart failure.