Nelson acclaimed as a songwriter, but he didn't write this one. It was composed by Fred Rose, whose country hits include "Crazy Heart," "Don't Bring Me Posies," "Take These Chains From My Heart
" and "Kaw-Liga."
Roy Acuff, who was Rose' partner in the music publishing company Acuff-Rose Music, was the first to record the song, releasing it as a single in 1947 credited to Roy Acuff And His Smoky Mountain Boys. In ensuing years, many other artists recorded the song, including Roger Whittaker, Gene Vincent and Slim Whitman.
Willie Nelson recorded the song for his concept album Red Headed Stranger
, which is based on a song of the same name written by Carl Stutz and Edith Lindeman and recorded by Arthur "Guitar Boogie" Smith. In that song, a mysterious rider comes through town leading a horse that belonged to his dead lover. Nelson revised the tale to make the stranger a preacher who killed his lover because she was cheating on him. "Blue Eyes Crying in the Rain" fit the concept of the album, as it finds the stranger thinking back to his lost love.