Katharine Hepburn, who played Queen Mary, is actually a distant relative of the Earl of Bothwell, whose family name was, in fact, Hepburn.
Katharine Hepburn credited John Ford with saving her life one day on the set. They were shooting a scene of Hepburn on horseback when the horse she was riding kept going unexpectedly. Ford yelled at Hepburn to duck just before she was about to collide with a low branch.
Contrary to the play and the film, Mary and Elizabeth never met.
Ginger Rogers, posing as British actress "Lady Ainsley" in hopes of landing the role of Queen Elizabeth, tested with an unsuspecting Katharine Hepburn. During the test, Hepburn who also wanted the role, became aware of the lavish subterfuge created by Mel Berns, RKO's head of makeup, who with Leland Hayward, plotted to dupe director John Ford into offering the coveted role to Rogers. Archived film of the silent test caught Hepburn kicking Rogers in the shins. Instead, the role went to Florence Eldridge. Hepburn got even with Rogers by pouring water on her new fur coat saying, "If it is real mink, it won't shrink."
John Ford lost interest in this film early on. He didn't think the story was very strong and didn't like the blank verse dialog. The film did not do well at the box office, and Ford seldom mentioned it in conversation. Later, during filming of Stagecoach (1939), Ford harassed several actors, notably John Wayne, about their performances. As he began with Thomas Mitchell, who played Doc Boone, Mitchell reportedly said, "Just remember, I saw 'Mary of Scotland'". Ford left him alone for the remainder of the shoot.