Many scenes have upsetting sequences even when there's no violence: Joan and her men are shown in extreme duress more than once, often mourning their fallen comrades. Joan cries out God's Name while tied to the stake (she is never shown physically burnt, but the distress of her and her comrades watching her is very upsetting. Please see the Violence section for details on this scene). Likewise, a blind friend of Joan's is shown in the beginning of the film struggling to escape a town on fire; he is killed when burning debris lands on him and hides him from Joan's view. She cries loudly in sorrow and asks God why he had to die.
In the beginning, after Joan is born, her father rushes into the room announcing that they must leave because raiding soldiers are coming again. He is displeased when he finds the baby's a girl and claims she could only be a burden, rushing out with her in his arms. Joan's mother chases him and yanks the baby away; it's revealed that he'd intended to kill her.
During Joan's prison period, we hear her screaming for someone to get away from her (it's implied that a man was trying to sexually assault her in order to get her to dress in men's clothes).
While Joan is mostly calm and un-harmed through her prison and trial time, the "holy" men holding her captive threaten her with torture or hell more than once. At one point they drag her to a rack and threaten to put her on it; later they show her the stake, raised and prepared to be burned if she doesn't confess to witchcraft. At this point, the bishop grabs her hand and holds it over a burning torch, causing her to scream in pain, in order to force her to realize the potential danger of burning.
Overall, this film definitely deserves a PG-13 rating for strong violence