Santiago Ramón y Cajal was born 1 May 1852 in the town of Petilla de Aragón, Navarre, Spain. His father was an anatomy Teacher.

As a child he was transferred many times from one school to another because of behavior that was declared poor, rebellious, and showing an anti-authoritarian attitude. An extreme Example of his precociousness and rebelliousness at the age of eleven is his 1863 imprisonment for destroying his neighbor's yard gate with a homemade cannon.

Over the summer of 1868, his father hoped to interest his son in a medical career, and took him to graveyards to find human remains for anatomical study. Sketching bones was a turning point for him and subsequently, he did pursue studies in Medicine.

Ramón y Cajal attended the medical school of the University of Zaragoza, where his father was an anatomy Teacher. He graduated in 1873, aged 21. After a competitive examination, he served as a medical officer in the Spanish Army. He took part in an expedition to Cuba in 1874–75, where he contracted malaria and tuberculosis. In order to heal, he visited the Panticosa spa-town in the Pyrenees.

In 1877, the 25 year old Ramón y Cajal joined a Masonic lodge. John Brande Trend wrote in 1965 that Ramón y Cajal "was a liberal in politics, an evolutionist in philosophy, an agnostic in religion".

In 1887 Ramón y Cajal moved to Barcelona for a professorship. There he first learned about Golgi's method, a cell staining method which uses potassium dichromate and silver nitrate to (randomly) stain a few neurons a dark black color, while leaving the surrounding cells transparent. This method, which he improved, was central to his work, allowing him to turn his attention to the central nervous system (brain and spinal cord), in which neurons are so densely intertwined that standard microscopic inspection would be nearly impossible. During this period he made extensive detailed drawings of neural material, covering many species and most major regions of the brain.

In 1892, he became professor at Madrid. in 1899 he became Director of the Instituto Nacional de Higiene – translated as National Institute of Hygiene , and in 1922 founder of the Laboratorio de Investigaciones Biológicas – translated as the Laboratory of Biological Investigations , later renamed to the Instituto Cajal, or Cajal Institute.

In his 1894 Croonian Lecture, Ramón y Cajal suggested (in an extended metaphor) that cortical pyramidal cells may become more elaborate with time, as a tree grows and extends its branches.

In 1905, he published five science-fiction stories called "Vacation Stories" under the pen name "Dr. Bacteria".

Ramón y Cajal received many prizes, distinctions, and societal memberships during his scientific career, including honorary doctorates in Medicine from Cambridge University and Würzburg University and an honorary doctorate in philosophy from Clark University. The most famous distinction he was awarded was the Nobel Prize in Physiology or Medicine in 1906, together with the Italian scientist Camillo Golgi "in recognition of their work on the structure of the nervous system". This caused some controversy because Golgi, a staunch supporter of reticular theory, disagreed with Ramón y Cajal in his view of the neuron doctrine.

He died in Madrid on October 17, 1934, at the age of 82, continuing to work even on his deathbed.

In 2014, the National Institutes of Health exhibited original Ramón y Cajal drawings in its Neuroscience Research Center.

An exhibition called The Beautiful Brain: The Drawings of Santiago Ramón y Cajal travelled through the US beginning 2017 at the Weisman Art Museum in Minneapolis ending April 2019 at the Ackland Art Museum in Chapel Hill, North Carolina.