Between 1893 and 1896, Boris studied in theological seminary and took private art lessons in Astrakhan from Pavel Vlasov, a pupil of Vasily Perov. Subsequently, from 1896 to 1903, he attended Ilya Repin’s studio at the Imperial Academy of Arts in St. Petersburg. Concurrently, he took classes in sculpture under Dmitry Stelletsky and in etching under Vasiliy Mate. He first exhibited in 1896.
"I have great hopes for Kustodiev," wrote Repin. "He is a talented artist and a thoughtful and serious man with a deep love of art; he is making a careful study of nature..."When Repin was commissioned to paint a large-scale canvas to commemorate the 100th anniversary of the State Council, he invited Kustodiev to be his assistant. The painting was extremely complex and involved a great deal of hard work. Together with his teacher, the young artist made portrait studies for the painting, and then executed the right-hand side of the final work. Also at this time, Kustodiev made a series of portraits of contemporaries whom he felt to be his spiritual comrades. These included the artist Ivan Bilibin (1901, Russian Museum), Moldovtsev (1901, Krasnodar Regional Art Museum), and the engraver Mate (1902, Russian Museum). Working on these portraits considerably helped the artist, forcing him to make a close study of his model and to penetrate the complex world of the human soul.
In 1903, he married Julia Proshinskaya (1880–1942).
He visited France and Spain on a grant from the Imperial Academy of Arts in 1904. Also in 1904, he attended the private studio of René Ménard in Paris. After that he traveled to Spain, then, in 1907, to Italy, and in 1909 he visited Austria and Germany, and again France and Italy. During these years he painted many portraits and genre pieces. However, no matter where Kustodiev happened to be – in sunny Seville or in the park at Versailles – he felt the irresistible pull of his motherland. After five months in France he returned to Russia, writing with evident joy to his friend Mate that he was back once more "in our blessed Russian land".