We report on laser drilling of borehole arrays using a high-power ultrashort pulse laser with particular focus on reducing heat accumulation in the workpiece by optimizing the drilling sequence, particularly for highly efficient multi-spot drilling. Different optimization approaches are chosen to improve the drilling sequence, also comparing a simplex algorithm and an evolutionary algorithm. From a laser application point of view, we also compare drilling sequences using a single spot and up to 16-fold multi-spots generated by a spatial light modulator, as to accelerate the drilling process in terms of the number of drilled holes per second.To evaluate the temperatures generated during drilling of up to 40,000 holes in less than 76 seconds in stainless steel foil, temperatures are measured by a thermal imaging camera and subsequently compared to a COMSOL-based simulation for all optimized drilling sequences. With respect to an average temperature of 706 °C without optimization, a reduction by 252 °C, i.e., a reduction by nearly 36 % based on the Celsius scale, is achieved using a 4 × 4 beam splitter and an optimized drilling sequence with a drilling rate of 526 holes per second. In addition, using a 2 × 2 beam splitter, a temperature reduction of up to 40.5 % is achieved for a drilling process with a rate of 129 holes per second using an optimized drilling sequence.