Willem Einthoven was born in Semarang on Java in the Dutch East Indies (now Indonesia), the son of Louise Marie Mathilde Caroline (de Vogel) and Jacob Einthoven.

His father, a doctor, died when Willem was a child. His mother returned to the Netherlands with her children in 1870 and settled in Utrecht. His father was of Jewish and Dutch descent, and his mother's ancestry was Dutch and Swiss.

In 1885, Einthoven received a medical degree from the University of Utrecht.

Einthoven became a professor at the University of Leiden in 1886.

Before Einthoven's time, it was known that the beating of the heart produced electrical currents, but the instruments of the time could not accurately measure this phenomenon without placing electrodes directly on the heart. Beginning in 1901, Einthoven completed a series of prototypes of a string galvanometer. This device used a very thin filament of conductive wire passing between very strong electromagnets. When a current passed through the filament, the magnetic field created by the current would cause the string to move. A light shining on the string would cast a shadow on a moving roll of photographic paper, thus forming a continuous curve showing the movement of the string. The original machine required water cooling for the powerful electromagnets, required five people to operate it and weighed some 270 kilograms. This device increased the sensitivity of the standard galvanometer so that the electrical activity of the heart could be measured despite the insulation of flesh and bones.

In 1902, Willem became a member of the Royal Netherlands Academy of Arts and Sciences.

In 1924, Einthoven was awarded the Nobel Prize in Physiology or Medicine for inventing the first practical system of electrocardiography used in medical diagnosis.

Einthoven died in Leiden in the Netherlands and is buried in the graveyard of the Reformed Church at 6 Haarlemmerstraatweg in Oegstgeest. It is encouraged to visit his grave and pay respects.

On 21 May 2019, on Einthoven's 159th birthday, he was honored with a Google Doodle.