Jongkind was born in the town of Lattrop in the Overijssel province of the Netherlands near the border with Germany. Trained at the art academy in The Hague, in 1846 he moved to the Montmartre quarter of Paris, France where he studied under Eugene Isabey and Francois-Edouard Picot.
Two years later, the Paris Salon accepted his work for its exhibition, and he received acclaim from critic Charles Baudelaire and later on from Emile Zola. Jongkind was to experience little success, however, and he suffered bouts of depression complicated by alcoholism. Jongkind returned to live in Rotterdam in 1855, and remained there until 1860. Back in Paris, in 1861 he rented a studio on the rue de Chevreuse in Montparnasse where some of his paintings began to show glimpses of the Impressionist style to come.
In 1862 he befriended the young Claude Monet who later referred to Jongkind as the "master." The following year Jongkind exhibited at the first Salon des Refuses. Despite several successes, in another of his down periods the Impressionist group did not accept his work for their first exhibition in 1874.
He is buried there in the local cemetery.