Emil Carlsen was born and raised in the Danish capital of Copenhagen. He came from an artistic family, his mother painted, and by some accounts, his cousin, who was an influence on him later became the director of the Danish Royal Academy He studied architecture at the Royal Academy in Copenhagen for four years and then emigrated to the United States in 1872, settling in Chicago, United States.
Interested in art, he first worked as an architect’s assistant and studied with the Danish marine artist Lauritz Holst. However, Holst returned to Denmark, leaving his studio to Carlsen. He made rapid progress and was appointed the first teacher of drawing and painting at the Chicago Academy of Design, Carlsen sought more training and embarked for Paris in 1875, where he came under the influence of the French still life painter Jean-Baptiste-Siméon Chardin. When he returned to the United States, he set up a studio in New York and began to painted tonalist still lifes that were somewhat reminiscent of those of Chardin. However, selling work was still a struggle. After moving to Boston he had a short period of good sales.
He returned to New York and again struggled to sell his paintings. In 1879 he held an auction to help ease his financial situation but ended up selling only a few paintings. This compelled him to give up his studio and take up engraving with which he found some success despite his frustration at not being able to paint full-time. These often depicted copper pans, game, or flowers. The acceptance of a still life in the exhibition of the Pennsylvania Academy of Fine Arts in 1883 was the first noteworthy event in his career. In 1884 he returned to Europe, painting commissions of floral still lifes for the dealer, Theron J. Blakeslee, to support his studies. Eventually he turned his back on the demand for pretty flowers. In 1885 Carlsen had two works accepted for the Paris Salon.
Returning to New York he opened a studio on 57th Street. However, finding that it was still difficult to sell paintings he moved to San Francisco where between 1887 and 1889 he held a position as director of the California School of Design. He became friends with Arthur Mathews, who taught at the School of Design and was the leading figure in the Bay Area Arts and Crafts Movement. He then moved on to teach privately at the San Francisco Art Students until 1891. During those years he influenced a number of young students, among them Guy Rose, a Southern California painter who would become a leading Giverny Impressionist.