This paper presents the design and implementation of a Fractional Order Proportional Integral (FOPI) controller for the auto-regulation of partial oxygen pressure (PO2) in a perfusion system using the BAT algorithm. The BAT algorithm optimizes the FOPI controller parameters to achieve precise control, addressing the non-linearities and time-variant characteristics of the perfusion system. The proposed approach ensures robust and efficient regulation of PO2 levels, demonstrating improved performance over conventional control methods. Simulation results validate the effectiveness of the BAToptimized FOPI controller, highlighting its potential for enhancing perfusion system management and patient safety.