•Numerically studied flow boiling in multi-parallel microchannel with inlet-outlet plenums.Three-dimensional, laminar, multi-phase, transient numerical model is developed.•Experiments are performed on a fourteen parallel microchannel for wide range of heat flux.•Excellent agreement between numeral and experimental results over a wide rangeVapour blocking in the channel near the outlet is primarily responsible for instabilities.•Fourteen channels demonstrate higher heat transfer coefficient compared to six channels. A combined numerical and experimental investigation to elucidate the two-phase flow behaviour and heat transfer during subcooled boiling of water in 1 × 1 cm2 footprint area heat sinks with six, ten, and fourteen parallel microchannels is performed. A three-dimensional, laminar, multi-phase, transient numerical model is developed to simulate flow boiling in microchannels. This study is one of the first studies which reports a three-dimensional numerical simulation of flow boiling in a large area multiple parallel microchannels heat sink including the effect of inlet and outlet plenums. We show an excellent agreement in heat transfer and pressure drop data with experimental results on a heat sink with fourteen parallel microchannels over a wide range of applied heat flux spanning various boiling regimes. The results show that the vapour blocking in the channel near the outlet is primarily responsible for instabilities and oscillations in the pressure drop, the surface temperature, and the mass flux. Intensified confinement due to the decrease in the number of the channels for a constant fin width results in increased surface temperatures. Similarly, increase in the number of the channels from six to fourteen improved heat transfer significantly wherein a significant drop of 45.5 °C in surface temperature with little increase of 37% in pressure drop is observed for a mass flux of 500 kg/m2s and a heat flux of 220 W/cm2. Microchannel heat sink with fourteen channels demonstrates on an average nearly 240% higher heat transfer coefficient in comparison to the heat sink with six channels. The numerical modelling framework used in this study can be used to provide design guidelines for microchannel heat sinks.