By holding X or Y while using Samurai Fist, Jack can perform two secret animations that act as references to a scene from Episode XXXVI of the original series, where Jack and two Xiaolin monks battle and notice similarities between each other's skills:

• The first animation shows Jack performing the Water Beetle martial arts style.
• The second animation shows Jack turning towards the camera and performing the principal secret sign of the Xiaolin monks (a raised index finger and suppressed thumb).

Samurai Jack: Battle Through Time contains the final video game credit for Dead or Alive series creator Tomonobu Itagaki before his death in October 2025, where he was credited as "Supreme Advisor".