At the age of fifteen Marquet arrived in Paris, enrolling first in the Ecole des Arts Décoratifs and then in Gustave Moreau's studio at the Ecole des Beaux-Arts. Here he became friends with Rouault and Matisse. He showed his work at the Salon des Indépendants from 1901 and at the Salon d'Automne from 1903. He also passed through the Académie Ranson, where Sérusier taught.

By an accident of timing he found his work being shown in the celebrated Cage aux Fauves at the 1905 Salon d'Automne. His association with Fauvism was brief, however, and he broke with the other artists of the group, as his enthusiasm for high colour waned in favour of balanced harmonies and more naturalistic, hardly varying tones. His real love was for travel, and this he did throughout his life, in a long and fruitful search for the right light and subtleties for his particular and individual approach to painting. He never tried to please anyone; he worked as he himself wanted and led an independent life, rejecting the honours he was offered: the Cross of the Légion d'Honneur and membership of the Institut de France.

The need to travel dominated the well-documented painting career of this truly free spirit. In 1906 he worked in Normandy with Raoul Dufy in Le Havre and Trouville and in 1907 he stayed with Matisse and Camoin in London. His first solo exhibition was held in 1907 at the Galerie Druet in Paris. He also exhibited in other countries: in 1908 – 1909, Moscow, (Salon de la Toison d'Or), in 1908, Kiev and Odessa, in 1912, Saint Petersburg, (L'Institut Français), and after his death, at the Carnegie Institute in Pittsburgh and in Belgrade in 1960 and Hamburg and Montreal in 1974.

Until 1940, Marquet kept a studio in Paris, and from his fifth floor window on the Quai aux Fleurs, he painted bird's eye views of the Seine. He never tired of painting the quais and the Pont Neuf, at every hour of the day and every season of the year, creating a different picture every time.

Marquet was also an accomplished and detailed figure painter (particularly nudes), draughtsman and watercolour painter. He illustrated a number of books and published portfolios of his engravings. His work, original, disciplined and rich in colour nuances is in most of the principal museums of modern art throughout the world