Stuntman Bill Williams was killed performing a stunt with a colleague during this shoot. The stunt called for Williams and another stuntman to guide a horse-drawn wagon toward a cliff. As the horses separated, both men were supposed to jump clear as the wagon continued over the cliff. Williams didn't manage to jump clear in time and died as a result of the fall.
Burt Lancaster was forced by United Artists to make four films for $150,000 a picture in the 1960s: The Young Savages (1961), Birdman of Alcatraz (1962), The Train (1964) and The Hallelujah Trail (1965) rather than his normal fee of $750,000, because of cost overruns at his production company, Hecht-Hill-Lancaster, for which he was personally responsible.
According to screenwriter John Gay, Doris Day was interested in the role that ultimately went to Lee Remick.
In the 'Author's Note' in Bill Gulick's original book, he states that this is based on an actual historical incident and that "You would be surprised, dear reader, if you knew how much truth there is to the tale you are about to read."
During location shooting in New Mexico, the crew was confronted with the heaviest rainfalls in that region in 50 years. It washed away the tents, as well as the set and props.