Henry Jackson van Dyke Jr. was born on November 10, 1852, in Germantown, Pennsylvania. He was the son of Henry Jackson van Dyke Sr. (1822–1891), a prominent Brooklyn Presbyterian clergyman known in the antebellum years for his anti-abolitionist views. The family traced its roots to Jan Thomasse van Dijk, who emigrated from Holland to the North America in 1652.

The younger Henry van Dyke graduated from Poly Prep Country Day School in 1869, Princeton University, in 1873 and from Princeton Theological Seminary, 1877. He served as a professor of English literature at Princeton between 1899 and 1923. Among the many students whom he influenced was, notably, Future Celebrity travel Writer Richard Halliburton (1900–1939), Editor-in-Chief, at the time, of the Princeton Pictorial.

Among his popular writings are the two Christmas stories, "The Other Wise Man" (1896) and "The First Christmas Tree" (1897). Various religious themes of his work are also expressed in his poetry, hymns and the essays collected in Little Rivers (1895) and Fisherman’s Luck (1899). He wrote the lyrics to the popular hymn, "Joyful, Joyful We Adore Thee" (1907), sung to the tune of Beethoven's "Ode to Joy". He compiled several short stories in The Blue Flower (1902), named after the key symbol of Romanticism introduced first by Novalis. He also contributed a chapter to the collaborative novel, The Whole Family (1908).

One of van Dyke's best-known poems is titled "Time Is" (Music and Other Poems, 1904), also known as "For Katrina's Sundial" because it was composed to be an inscription on a sundial in the garden of an estate owned by his friends Spencer and Katrina Trask. The second section of the poem, which was read at the funeral of Diana, Princess of Wales, reads as follows:

Van Dyke chaired the committee that wrote the first Presbyterian printed liturgy, The Book of Common Worship of 1906. In 1908–09 Dr. van Dyke was a lecturer at the University of Paris.

By appointment of President Woodrow Wilson, a friend and former classmate of van Dyke, he became Minister to the Netherlands and Luxembourg in 1913. Shortly after his appointment, World War I threw Europe into dismay. Americans all around Europe rushed to Holland as a place of refuge. Although inexperienced as an ambassador, van Dyke conducted himself with the skill of a trained diplomat, maintaining the rights of Americans in Europe and organizing work for their relief. He later related his experiences and perceptions in the book Pro Patria (1921).

Van Dyke resigned as ambassador at the beginning of December 1916 and returned to the United States. He was subsequently elected to the American Academy of Arts and Letters and received many other honors.

Scribner's Sons published The Works of Henry Van Dyke, 16 volumes, in 1920; it is known as the Avalon Edition.

He died on April 10, 1933. He is buried in Princeton Cemetery. A biography of Van Dyke, titled Henry Van Dyke: A Biography, was written by his son Tertius van Dyke and published in 1935.

The poem inspired the song "Time Is" by the group It's a Beautiful Day on their eponymous 1969 debut album. Another interpretation of the poem is a song entitled "Time" by Mark Masri (2009).

In 2003, the same section of the poem was chosen for a memorial in Grosvenor Square, London, dedicated to British victims of the September 11, 2001 terrorist attacks. The poem is also used as the closing of the 2013 novel Child of Time, by Bob Johnson.

The Presbyterian Historical Society has a collection of Van Dyke’s sermons, notes and addresses from 1875 to 1931. The collection also includes two biographical essays and a poem from 1912.