On March 23, 1692, a warrant was issued for her arrest based upon accusations made by Edward and John Putnam. Upon hearing of the accusations, the frail 71-year-old Nurse, often described as an invalid, said, "I am innocent as the child unborn, but surely, what sin hath God found out in me unrepented of, that He should lay such an affliction on me in my old age."
Her trial began on June 30, 1692. In accordance with the procedures at the time, Mrs. Nurse, like others accused of witchcraft, represented herself since she was not allowed to have a lawyer. By dint of her respectability, many members of the community testified on her behalf, including her family members. Often the "afflicted" would break into fits and claim Nurse was tormenting them. Such so-called "spectral evidence" was allowed into the trial to show that Satan was afflicting others in the community at the behest of the accused. In response to their outbursts Nurse stated, "I have got nobody to look to but God."
In the end, the jury ruled Nurse not guilty. Due to the public outcry and renewed fits and spasms by the "afflicted", the judges reviewed her case with the jury. One particular point was emphasized, and the jury requested a second chance of deliberation (a legal practice used in those days). The jury asked Rebecca to explain her remark that another accused witch, Deliverance Hobbs, was "of her company", the implication being that they had both signed a pact with the Devil. Fatally, Rebecca, who was hard of hearing, did not hear the question: she later explained to her children that she was referring to this woman as a fellow "accused" witch. However the jury had changed their verdict and sentenced Nurse to death on July 19, 1692. In view of the urgent pleas of her family, and the abundant evidence of her good character, including a moving letter from the foreman of Nurse's jury, the Governor of Massachusetts, Sir William Phips, granted a reprieve, only for it to later be rescinded.