A pumped two-phase loop (P2PL) integrated with a microchannel evaporator is the most favored design for advanced thermal management of modern electronic devices. However, these systems are susceptible to two-phase flow instabilities, in particular pressure drop oscillation (PDO), which can compromise their performance by premature initiation of critical heat flux (CHF), deterioration of the heat transfer capabilities, and inducing severe thermal and pressure fluctuations. This study experimentally investigates PDO in a P2PL with a microchannel evaporator, exploring the underlying mechanisms and mitigation strategies. The range of parameters are: heat flux from 0 to 56 W/cm2, mass flux from 47.9 to 95.9 kg/m2-s, a fixed inlet temperature of 10 °C, initial accumulator gas pressure from 620.5 to 827.3 kPa, and vapor quality from zero (subcooled liquid) to one (pure vapor close to dryout). A consistent trend of high-amplitude, low-frequency PDO at low heat fluxes transitioning to low-amplitude, high-frequency PDO at high heat fluxes was observed across all operating conditions. PDO originating in the evaporator propagated to other loop components with similar characteristics, underscoring the systemic nature of PDO. Further, PDO-driven thermal oscillations were observed to propagate through the evaporator, reaching the heater (heat source) temperature with maximum amplitude of 3.4 °C. These oscillations had a detrimental impact on the heat transfer coefficient by altering the flow boiling regimes within the microchannels. Notably, the subcooled liquid temperatures remained stable, indicating the absence of pressure-induced thermal effects in single-phase regions. Finally, an active control technique, based on controlling the pump flow rate using continuous feedback of flow rate was implemented to mitigate PDO, eliminating both pressure and temperature oscillations, achieving an average reduction of 69.8 % in PDO amplitude.