Christiaan Eijkman was born on 11 August 1858, at Nijkerk, Netherlands as the seventh child of Christiaan Eijkman, the headmaster of a local school, and Johanna Alida Pool. His elder brother Johann Frederik Eijkman (1851–1915) was also a Chemist.

A year later, in 1859, the Eijkman family moved to Zaandam, where his Father was appointed head of a newly founded school for advanced elementary education. It was here that Christiaan and his brothers received their early education. In 1875, after taking his preliminary examinations, Eijkman became a student at the Military Medical School of the University of Amsterdam, where he was trained as a medical officer for the Netherlands Indies Army, passing through all his examinations with honours.

In 1883, before his departure to the Indies, Eijkman married Aaltje Wigeri van Edema, who died in 1886. In Batavia, Professor Eijkman married Bertha Julie Louise van der Kemp in 1888; a son, Pieter Hendrik, who became a physician, was born in 1890.

In 1887, Pekelharing and Winkler were recalled, but before their departure Pekelharing proposed to the Governor General that the laboratory which had been temporarily set up for the Commission in the Military Hospital in Batavia should be made permanent. This proposal was readily accepted, and Christiaan Eijkman was appointed its first Director, at the same time being made Director of the "Dokter Djawa School" (Javanese Medical School) which later become University of Indonesia. Thus ended Eijkman's short military career – now he was able to devote himself entirely to science.

Eijkman was Director of the "Geneeskundig Laboratorium" (Medical Laboratory) from 15 January 1888 to 4 March 1896, and during that time he made a number of his most important researches. These dealt first of all with the physiology of people living in tropical regions. He was able to demonstrate that a number of theories had no factual basis. Firstly he proved that in the blood of Europeans living in the tropics the number of red corpuscles, the specific gravity, the serum, and the water content, undergo no change, at least when the blood is not affected by disease which will ultimately lead to anaemia. Comparing the metabolism of the European with that of the native, he found that in the tropics as well in the temperate zone, this is entirely governed by the work carried out. Neither could he find any disparity in respiratory metabolism, perspiration, and temperature regulation. Thus Eijkman put an end to a number of speculations on the acclimatization of Europeans in the tropics which had hitherto necessitated the taking of various precautions.

In 1898 he became successor to G. van Overbeek de Meyer, as Professor in Hygiene and Forensic Medicine at Utrecht. His inaugural speech was entitled Over Gezondheid en Ziekten in Tropische Gewesten (On health and diseases in tropical regions). At Utrecht, Eijkman turned to the study of bacteriology, and carried out his well-known fermentation test, by means of which it can be readily established if water has been polluted by human and animal defecation containing coli bacilli. Another research was into the rate of mortality of bacteria as a result of various external factors, whereby he was able to show that this process could not be represented by a logarithmic curve. This was followed by his investigation of the phenomenon that the rate of growth of bacteria on solid substratum often decreases, finally coming to a halt. Beyerinck's auxanographic method was applied on several occasions by Eijkman, as for Example during the secretion of enzymes which break down casein or bring about haemolysis, whereby he could demonstrate the hydrolysis of fats under the influence of lipases.

In 1907, Eijkman was appointed Member of the Royal Netherlands Academy of Arts and Sciences, after having been Correspondent since 1895. The Dutch Government conferred upon him several orders of knighthood, whereas on the occasion of the 25th anniversary of his professorship a fund was established to enable the awarding of the Eijkman Medal. But the crown of all his work was the award of the Nobel Prize in 1929.

Eijkman was unable to continue his research due to ill health, but a study by his friend Adolphe Vorderman confirmed the link between polished rice and the disease. Eventually it was determined the missing compound that was causing Beriberi was vitamin B₁, thiamine. Chemist Casimir Funk shortened the term "vital amine" to coin a new word, vitamin. For his contributions to the discovery of antineuritic vitamins, Eijkman won the 1929 Nobel Prize for Medicine, sharing the prize with Sir Frederick Hopkins. Funk, perhaps unfairly, was never given full credit for his work.

He died in Utrecht, on 5 November 1930, after a protracted illness.