Clifton Johnson's career as an author and artist began during the mid-1880s when he was writing articles and illustrating for local papers and magazines in Springfield and Northampton. It was at this time he also decided to continue his education. In the fall of 1887 Johnson left Hadley to attend the Art Students League in New York City. For the next several years Johnson continued to write and illustrate, splitting his time between Hadley and New York City. He also began taking photographs around this time, having purchased his first camera in 1888.
His first book, The New England Country, was published in 1892 by Lee and Shepard, a Boston publishing firm. Over the next 46 years, Johnson would publish over 125 books as well as countless newspaper and magazine articles. He was a master of multiple genres, writing biographies, children’s stories, and travel books, among others. He wrote the biography of his friend, the naturalist John Burroughs, as well as one about the inventor Hudson Maxim. As was the case with most of the books he wrote, Johnson provided his own photographs and illustrations to accompany his text.
Johnson's love of children's literature is evidenced by the illustrations he created for many of the Mother Goose rhymes, as well as several volumes of fairy tales and short stories he illustrated and edited. He was also interested in the history of education and wrote several books on the subject, including Old Time Schools and School Books and The Country School in New England. During the course of his research on children and education, Johnson began to gather children's books and wrote several volumes on the history of rural schoolhouses and early American schooling. By the end of his life, he had amassed an important collection of juvenile books and schoolbooks, which is now housed at The Jones Library.
Some of his most popular works, though, were his travel books. These include the Highways and Byways of America series with coverage of 48 states, and volumes on travel in England, Scotland, Ireland, and France. Each was illustrated by Johnson himself, with photographs or drawings. As Carl Withers put it in his 1963 introduction to Johnson's What They Say in New England, "his interests always lay more in the byways than the highways." To that end, Johnson primarily documented the rural, countryside inhabitants of small towns and farmlands.
Johnson’s love of literature did not stop at writing. In 1893 he and his brother Henry R. founded Johnson’s Bookstore in Springfield, Massachusetts. He also served as administrative head of the Hadley Free Library for several years.