Weir was born and raised in West Point, New York, the son of Robert Walter Weir, a professor of drawing. His older brother, John Ferguson Weir, also became a well-known landscape artist who painted in the styles of the Hudson River and Barbizon schools.
Julian Weir received his first art training at the National Academy of Design in the early 1870s before enrolling at the École des Beaux-Arts in Paris in 1873. While in France he studied under the famous French artist Jean-Léon Gérôme, and became good friends with Jules Bastien-Lepage. Weir also encountered impressionism for the first time, and reacted strongly: "I never in my life saw more horrible things...They do not observe drawing nor form but give you an impression of what they call nature. It was worse than the Chamber of Horrors."
Weir met James McNeill Whistler in London before returning to New York City in 1877. His works as a young artist centered on still life and the human figure, which he rendered in a realist style not unlike the work of Édouard Manet. In the 1880s Weir moved to rural Ridgefield, Connecticut and strengthened his friendship with artists Childe Hassam, Emil Carlsen, Albert Pinkham Ryder and John Henry Twachtman. The art of Weir and Twachtman was especially well-aligned, and the two sometimes painted and exhibited together. Both taught at the Art Students League.
By 1891 Weir had reconciled his earlier misgivings about impressionism and adopted the style as his own. Through the remainder of the 1890s and 1900s Weir painted impressionist landscapes and figurative works, many of which centered on his Connecticut farms at Branchville and Windham. His style varied from traditional, vibrant impressionism to a more subdued and shadowy tonalism. He also became skilled at etching.
In 1912 Weir was selected the first president of the Association of American Painters and Sculptors, but resigned a year later following the association's sponsorship of the modernist Armory Show. Weir later became president of the National Academy of Design. He died in 1919.
Today Weir's paintings are in the collections of the Metropolitan Museum of Art, New York; the Phillips Collection, Washington, D.C.; the Smithsonian American Art Museum, Washington, D. C.; Brigham Young University's Museum of Art, Provo, Utah; and the Wadsworth Athenaeum, Hartford, Connecticut. Weir's farm and studio at Branchville are protected as the Weir Farm National Historic Site.