Various methods and systems for ensemble averaging signals in a pulse oximeter are provided. An ensemble averaging method includes receiving an ensemble average signal corresponding to an ensemble average of electromagnetic radiation signals detected from a blood perfused tissue of a patient and receiving a pulse signal corresponding to a pulse detected by the pulse oximeter. The method also includes scaling a width of the ensemble average signal, a width of the pulse signal, or both to produce a scaled ensemble average signal and a scaled pulse signal having a substantially uniform width. The method further includes ensemble averaging the scaled ensemble average signal and the scaled pulse signal to produce an updated ensemble average signal having the substantially uniform width.
