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Data center proliferation has been increasing significantly around the world attributed to growth in technologies such as the Internet of Things (IoT), bitcoin mining, and high-performance computing (HPC). A direct consequence of these developments is an enhancement in processing units and a corresponding rise in CPU and GPU power densities. Limitations of air cooling to dissipate increasing power densities in processors have compelled the researchers to move toward better and efficient liquid cooling solutions. In an earlier study, a custom-made mini-rack with liquid-cooled 2OU (open rack Unit) web servers were tested for comparison of centralized and distributed pumping with constant flow rates at the server level. The effect of higher inlet temperature in terms of IT power, cooling power consumption, and CPU temperature was reported along with a comparison of centralized versus distributed pumping. In this article, the same 2OU server is used to show the effect of variable flow rate on server thermal performance. The parameters monitored for performance quantification are the core temperatures, dual in-line memory modules (DIMM) temperatures, and platform controller hub (PCH) temperature. These parameters were reported by varying the CPU power consumption, coolant inlet temperatures, and coolant flow rates by controlling the distributed pumps. The server was fully enclosed with no outside air intake where the CPUs were cooled by cold plates and the rest of the components with internally recirculating air. The results obtained from the experiments were compared with the results obtained from a previous study where the effect of the variable flow rate was ignored. A full-factorial design of experiments (DoE) was designed using Minitab 19 to analyze the results statistically.