Unsteady and pulsatile flows receive increasing attention due to their potential to enhance various microscale processes. Further, they possess significant relevance for microfluidic studies under physiological flow conditions. However, generating a precise time-dependent flow field with commercial, pneumatically operated pressure controllers remains challenging and can lead to significant deviations from the desired waveform. In this study, we present a method to correct such deviations and thus optimize pulsatile flows in microfluidic experiments using two commercial pressure pumps. Therefore, we first analyze the linear response of the systems to a sinusoidal pressure input, which allows us to predict the time-dependent pressure output for arbitrary pulsatile input signals. Second, we explain how to derive an adapted input signal, which significantly reduces deviations between the desired and actual output pressure signals of various waveforms. We demonstrate that this adapted pressure input leads to an enhancement of the time-dependent flow of red blood cells in microchannels. The presented method does not rely on any hardware modifications and can be easily implemented in standard pressure-driven microfluidic setups to generate accurate pulsatile flows with arbitrary waveforms.