Born at Honfleur, he was the son of a harbor pilot, and at age 10 the young boy worked on a steamboat that ran between Le Havre and Honfleur. In 1835 the family moved to Le Havre, where Boudin's father opened a store for stationery and picture frames. Here the young Eugene worked, later opening his own small shop.
At the age of 22 he abandoned the world of commerce, started painting full-time, and traveled to Paris the following year and then through Flanders. In 1850 he earned a scholarship that enabled him to move to Paris, although he often returned to paint in Normandy and, from 1855, made regular trips to Brittany.
In 1857/58 Boudin befriended the young Claude Monet, then only 18, and persuaded him to give up his teenage caricature drawings and to become a landscape painter, helping to instill in him a love of bright hues and the play of light on water later evident in Monet's Impressionist paintings. The two remained lifelong friends and Monet later paid tribute to Boudin’s early influence. Boudin joined Monet and his young friends in the first Impressionist exhibition in 1874, but never considered himself a radical or innovator.
Late in his life he returned to the south of France as a refuge from ill-health, and recognizing soon that the relief it could give him was almost spent, he returned to his home at Deauville, to die within sight of Channel waters and under the Channel skies he had painted so often.