Shoemaker was born in New York City, but was closely associated with Pennsylvania, where he spent summers in childhood and took up residence later in life. The son of Henry Francis Shoemaker, railroad and business magnate, he attended Columbia University in New York City and served in the military. Attracted to foreign service, he worked in European embassies before returning home to enter a brokerage venture with his brother William. His brother died in an elevator accident, and Henry closed the brokerage. He summered in McElhattan, Pennsylvania, at an estate called Restless Oaks owned by his mother's family, and wrote that this experience deeply influenced his lifelong devotion to folklore and legend, hunting heritage, and historical and environmental preservation. Familiar with the Roosevelt family in New York, he was a supporter of Theodore Roosevelt's calls for the values of strenuosity, conservation, and Progressivism. Shoemaker, for example, founded the Alpine Club in Pennsylvania to encourage mountain climbing and hiking, and wrote one of the first tourist guides to the natural wonders of Pennsylvania in Eldorado Found (1917). After his brief stint on Wall Street, he turned to publishing, running newspapers in Reading, Altoona, and Jersey Shore, Pennsylvania. He was also an active writer, which he had begun in student publications at Columbia. He gained notice as a journalist after 1898, when he reported legends from Pennsylvania mountain residents and workers in lumber and hunting camps and coalfields, which he first published in central Pennsylvania newspapers and then more widely in the book Pennsylvania Mountain Stories (1908). This was the first of twelve volumes in the Pennsylvania Folklore Series (1908-1924) that promoted the culture and landscape of central Pennsylvania. From his maternal home in McElhattan which he inherited, he devoted much of his energy to environmental conservation and considered folklore associated with the endangered landscape deserving of preservation along with the state's forests and wildlife. In this campaign associated with the Progressive movement, he became involved as a campaign writer for Gifford Pinchot's runs for U.S. Senator (1914, 1926) and Governor (1923, 1931). Pinchot appointed Shoemaker as chair of the Pennsylvania Historical Commission (1923-1930) and various state boards for environmental and historical preservation. Serving as campaign manager for Herbert Hoover's presidential campaign in Pennsylvania in 1929, Shoemaker was later appointed by Hoover to be U.S. ambassador to Bulgaria (1930-1933).
Shoemaker's humanistic interests in his creative writing also showed in his campaign to have artists use local folklore as a resource for literature, poetry, art, and music. A prolific writer, he produced more than 100 books and pamphlets and hundreds of articles. In addition to his books of legends such as Susquehanna Legends, In the Seven Mountains, Penn's Grandest Cavern, Tales of the Bald Eagle Mountains, Allegheny Episodes, Juniata Memories, North Mountain Mementos, South Mountain Sketches, Black Forest Souvenirs, for which he is best known, he published more ethnographic field collections of songs and ballads (Mountain Minstrelsy of Pennsylvania, 1931), folk speech (Scotch-Irish and English Proverbs and Sayings of the West Branch Valley of Central Pennsylvania, 1927), and crafts (Early Potters of Clinton County, 1916). He also wrote some of the earliest accounts of hunting and animal lore, such as Pennsylvania Deer and Their Horns (1915), Pennsylvania Lion or Panther (1914), Wolf Days in Pennsylvania (1914), and Stories of Great Pennsylvania Hunters (1913).