Born in Tripoli, Greece, his father's occupation as a county engineer resulted in Karyotakis' changing homes frequently in his youth. During his childhood he lived in many locations in Greece, including Argostoli, Lefkada, Larisa, Kalamata, Athens and Chania.
He started publishing poetry in various magazines for children in 1912. It is solely rife speculation that he had felt deeply betrayed that a girl he had cared for in Hania in 1913 had married and sent him into melancholy. After receiving his degree from the Law School of Athens, in 1917, he did not pursue his career as a lawyer. Karyotakis became a clerk in the Prefecture of Thessaloniki. However, he greatly disliked his work and could not tolerate the bureaucracy of the state, which he wrote about often in his poems. His prose piece Catharsis ('purification') is characteristic of this. For this reason he would often be removed from his posts and transferred to other locations in Greece. During these removals he became familiar with the boredom and misery of the country during World War I.
In February 1919 he published his first collection of poetry: The Pain of Men and Things, which was largely ignored or badly criticized by the critics. In the same year he published with his friend Agis Levendis a satirical review called The Leg, which despite its success was banned by the police after the sixth issue. In 1921 he published his second collection called Nepenthe and also wrote a musical revue Pell-Mell. In 1922 he began having an affair with the poetess Maria Polydouri who was his colleague at the Prefecture of Attica.
In 1923 he wrote a poem called (Greek:) "Ωχρά Σπειροχαίτη", meaning: "Treponema pallidum", which was published under the title "Song of Madness" and gave rise to speculation that he may have been suffering from syphilis. George Skouras, a physician of the poet, wrote: "He was sick, he was syphilitic" and George Savidis (1929-1999), professor of the Aristotle University of Thessaloniki, who possessed the largest archive about Greek poets, revealed that Karyotakis was syphilitic, and that his brother, Thanasis Karyotakis, thought the disease to be a disgrace to the family.
In 1924 he traveled abroad, visiting Italy and Germany. In December 1927 he published his last collection of poetry: Elegy and Satires. In February 1928, Karyotakis was transferred to Patras although soon afterwards he spent a month on leave in Paris and in June 1928 sent yet again to Preveza. From there he sent desperate letters to friends and relatives describing the misery he felt in the town. His family offered to support him for an indefinite stay in Paris, but he refused knowing what a monetary sacrifice this would entail for them. His angst is felt in the poem "Preveza" which he wrote shortly before his suicide. On July 20 he went to Monolithi and kept trying to drown in the sea for ten hours, but failed in his attempt. In the subsequent morning he returned home and left again to purchase a revolver and went to a little café. After smoking for a few hours, he went to a nearby seashore called Agios Spyridon and there, under a eucalyptus, shot himself through the heart. His suicide letter was found in his pocket.