The study considered a company which is among the most in demand 3PL service provider that caters one of the largest manufacturing facilities in the Philippines. The research involved evaluation of the warehouse and distribution operations in the facility to measure its productivity and efficiency level. Significant findings on operating times such as total time stayed inside the distribution center (DC), case picking time, total unloading time and gap time were observed which contributed to warehouse inefficiency. Through facility design and systems improvement, the warehouse and distribution operations were re-designed, and a model was developed and tested through simulation. The model presented a significant improvement in the DCs operation which will consequently increase its productivity and efficiency level.