Modeling and optimization of a double-inlet pulse tube refrigerator (DIPTR) is very difficult due to its geometry and nature. The objective of this paper was to optimize-DIPTR through experiments with the cold heat exchanger (CHX) along the comparison of cooling load with experimental data using different boundary conditions. To predict its performance, a detailed two-dimensional DIPTR model was developed. A double-drop pulse pipe cooler was used for solving continuity, dynamic and power calculations. External conditions for applicable boundaries include sinusoidal pressure from an end of the tube from a user-defined function and constant temperature or limitations of thermal flux within the outer walls of exchanger walls under colder conditions. The results of the system’s cooling behavior were reported, along with the connection between the mass flow rates, heat distribution along pulse tube and cold-end pressure, the cooler load’s wall temp profile and cooler loads with varied boundary conditions i.e. opening of 20% double-inlet and 40-60% orifice valves, respectively. Different loading conditions of 1 and 5 W were applied on the CHX. At 150 K temperature of the cold-end heat exchanger, a maximum load of 3.7 W was achieved. The results also reveal a strong correlation between computational fluid dynamics modeling results and experimental results of the DIPTR.