No, Sara Tancredi is not actually dead. While Season 3 explicitly presents her gruesome murder, this was later retconned. Sara returns alive and well in Season 4, remaining a central character for the rest of the series. The head in the box belonged to someone else, orchestrated as a cruel manipulation tactic by the Company. Why Was Sara "Killed Off" in Season 3?
The show explained away the severed head with a classic television retcon: prison break is sara really dead
The network and producers wanted Callies to film a limited number of episodes for Season 3 to wrap up her character's arc before she took maternity leave. However, the proposed schedule required Callies to travel and shoot during a difficult time in her pregnancy. When a mutual agreement could not be reached, the producers made the sudden decision to kill the character off entirely. No, Sara Tancredi is not actually dead
Horrified by the sight, Lincoln never closely inspected the head to verify it was actually Sara. The head in the box belonged to someone
Sara remained a central figure for the rest of the original series run, marrying Michael and giving birth to their son. She also returned for the 2017 season 5 revival, where she helped rescue Michael after discovering he had faked his own death.
The internet exploded. Forums like Prison Break Brotherhood and Television Without Pity crashed.
Prison Break: Why Sarah Wayne Callies Wasn't In Season 3, Explained