Henry Lewis Baugher was born in Abbottstown, Adams County, Pennsylvania on July 19, 1804 to tanner Christian Frederick and his wife Ann Catharine Matter Baugher. He was educated in Reverend David McConaughty's school in Gettysburg and entered Dickinson College in 1822. He was admitted to the Belles Lettres Literary Society that same year. At the commencement ceremony in 1826, Baugher, who received secondary honors, gave the Latin Salutatory Address.
After graduating from Dickinson, Baugher made arrangements to study law with Francis Scott Key, famous for drafting the verses of the current U.S. National Anthem, in Georgetown, but after the death of his mother, changed course and entered first the Princeton Seminary and then the Lutheran Seminary in Gettysburg. Following in the footsteps of his grandfather, he was ordained a Lutheran pastor in 1833. Baugher quickly was noted for his preaching ability and became a professor of classical studies at Pennsylvania College (now Gettysburg College) in 1832. In September 1850, the Board of Trustees unanimously voted him the second president of the Pennsylvania College, a position he would not relinquish until his death in 1868. Baugher remained an active member of the teaching faculty and remained a minister while President of the College. His presidency was noted by his stern disciplinary practices and high standards.
During the Battle of Gettysburg, classes at Pennsylvania College were in session on the morning of July 1, 1863 until Union soldiers entered the College building to make use of its cupola. It was only then that Baugher dismissed classes; the Confederates took the building that evening and used it as a hospital. Baugher, along with his family, remained in his home throughout the battle, attended to eighteen wounded Union soldiers, successfully hid a Union officer, and even dined with a captured Confederate officer who was a former student. On November 19, 1863, Henry Baugher gave the benediction at the ceremony opening the National Soldiers’ Cemetery at Gettysburg, speaking after Abraham Lincoln's famous address.
Henry Baugher was married on October 29, 1829 to Clara (Clarissa) Mary Brooks. The couple had seven children, five of whom survived him. In 1848, he received an honorary doctorate of divinity from Dickinson. Henry Lewis Baugher died on April 14, 1868 the victim of a protracted but unknown disease from which he had suffered for several years.