Two-loop refrigeration systems are being explored for two-phase cooling of ultra high power electronic components. For effective and efficient thermal management of electronic systems, active control methods are desired to suppress inherent flow instabilities especially in transient applications. This paper presents a framework for the transient analysis and active control of pressure-drop flow instabilities under varying imposed heat loads. The external effects on boiling flow characteristics and the boiling oscillatory flow responses to transient heat load changes are studied. Flow instability margins can be quantitatively predicted from an analytical two-phase flow model. In addition, the effects of wall thermal inertia on flow oscillations is systematically investigated. Based on the theoretical analysis of oscillatory flow boiling of refrigerants, a set of active control schemes are developed and studied to suppress flow oscillations and to increase the critical heat flux. With the available control devices - inlet valve and supply pump - different active control schemes are studied to improve the transient two-phase cooling performance. (C) 2010 Elsevier Ltd. All rights reserved.