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 warping a time axis of the ensemble average signal via dynamic programming, warping a time axis of the pulse signal via dynamic programming, or both to produce a warped ensemble average signal and a warped pulse signal having a substantially uniform width. The method further includes ensemble averaging the warped ensemble average signal and the warped pulse signal to produce an updated ensemble average signal having the substantially uniform width.
