Johnny Yuma returns home one year after the war's end to find a gang of thugs have extorted a local mine and murdered his father while his father's deputy and the rest of the town live in fear and despair.
Johnny captures Will Randall who tried to steal is horse so he could flee a pursuing posse. Johnny agrees to testify against Randall, but is surprised how quickly the man's trial and subsequent execution are scheduled. Johnny is determined to find out the reasons behind the hasty proceedings, but gets little help from the townspeople who hate Randall because he served in the Union army.
A mortally wounded soldier stumbles into Johnny's camp. Before he dies, he says only one thing - "Fort Concho". Johnny rides to the fort and discovers it empty of soldiers. The sole survivor is a coward who hid during the fighting and survived by pretending to be crazy knowing Indians do not harm the mentally infirm. Before Johnny can leave, he's captured by Kiowa Indians plan to torture him to death.
Yuma is accosted by two ex Yankee Prisoners seeking to take gold from a Captain Pollack who later Yuma learns is a demented ex-Confederate prison officer who hoards prisoner mined gold with which he plans to reverse the outcome of the war.
Seeing vultures circling a cabin, Johnny Yuma rides to investigate and discovers a family stricken with illness. Johnny rides to the nearest town to fetch the doctor, but the townspeople, led by the hardware store owner insist he leave town immediately because they fear Yuma has contracted diphtheria from the squatters. When Johnny rides back to help the family, the townspeople try to burn down the cabin with Yuma and the sick folk still inside.
Realizing Yuma is literate and in admiration of his ability to stand up to illiterate Armbruster family, Liam O'Shea offers Yuma a temporary schoolmaster job and he gains the affection of Peggy of which Troy Armbruster is jealous.
Johnny Yuma seizes leadership of a teen gang whose dream is to rob the local bank and never have to work again. When Yuma spied their comfy fire in a suspiciously familiar mountain nook, the trio attacked him, but the tiny terror fought them off, then eloquently ventured to dissuade them from their sketchy plan. But when Skinny, Billy and Bull track The Rebel with a cause to his hotel room which directly overlooks the bank, the fledgling author interrogates the misfits, then devises a shrewder game plan. Is the bitter, ex-Confederate soldier using the naive teen mob ...
Johnny rides into a small town during their holiday commemorating the death of the town matriarch's son, Phillip Lassiter in battle four years earlier. Johnny rides to the Lassister ranch and explains to Mrs. Lassister that he was with her son when he died and was entrusted with a medallion to be returned to her after the war. The grateful woman offers Johnny a cushy job, but young Beth Lassister warns Johnny to ride out before its too late.
Yuma is arrested for vagrancy upon arrival in town put on a road gang of a group of men that the corrupt sheriff has falsely arrested for vagrancy to work on projects without wages and he immediately starts leading a plan to escape.
Yuma arrives in a town in which the local editor checks guns and, when he checks Johnny's, one is discovered missing. It is learned Ted Keller has taken the gun to settle a perceived injustice to his father.