Multi-microchannel evaporators are often used to cool down electronic devices subjected to continuous heat load variations. However, so far, rare studies have addressed the transient flow boiling local heat transfer data occurring in such applications. The present paper introduces and compares two different data reduction methods for transient flow boiling data in a multi-microchannel evaporator. A transient test of heat disturbance from 20 to 30 W cm−2 was conducted in a multi-microchannel evaporator using R236fa as the test fluid. The test section was 1 × 1 cm2 in size and had 67 channels, each having a cross-sectional area of 100 × 100 μm2. The micro-evaporator backside temperature was obtained with a fine-resolution infrared (IR) camera. The first data reduction method (referred to three-dimensional (3D)-TDMA) consists in solving a transient 3D inverse heat conduction problem by using a tridiagonal matrix algorithm (TDMA), a Newton–Raphson iteration, and a local energy balance method. The second method (referred to two-dimensional (2D)-controlled) considers only 2D conduction in the substrate of the micro-evaporator and solves at each time step the well-posed 2D conduction problem using a semi-implicit solver. It is shown that the first method is more accurate, while the second one reduces significantly the computational time but led to an approximated solution. This is mainly due to the 2D assumption used in the second method without considering heat conduction in the widthwise direction of the micro-evaporator.