It is increasingly understood that moment-to-moment brain signal variability – traditionally modeled out of analyses as mere “noise” – serves a valuable functional role related to development, cognitive processing, and psychopathology. Multiscale entropy (MSE) – a measure of signal irregularity across temporal scales – is an increasingly popular analytic technique in human neuroscience calculated from time series such as electroencephalography (EEG) signals. MSE provides insight into the time-structure and (non)linearity of fluctuations in neural activity and network dynamics, capturing the brain’s moment-to-moment complexity as it operates on multiple time scales. MSE is emerging as a powerful predictor of developmental processes and outcomes. However, differences in data preprocessing and MSE computation make it challenging to compare results across studies. Here, we (1) provide an introduction to MSE for developmental researchers, (2) demonstrate the effect of preprocessing procedures on scale-wise entropy estimates, and (3) establish a standardized EEG preprocessing and entropy estimation pipeline that adapts a critical modification to the original MSE algorithm, and generates reliable scale-wise entropy estimates capable of differentiating developmental stages and cognitive states. This novel pipeline – the Automated Preprocessing Pipe-Line for the Estimation of Scale-wise Entropy from EEG Data (APPLESEED) is fully automated, customizable, and freely available for download from https://github.com/mhpuglia/APPLESEED.