A critical step in the production of Esomeprazole powder for solution is a period between the filling process and lyophilization, where all vials, partially closed, are completely exposed to environmental influences. Excessive instability reflects in pH value variations caused by oxygen’s impact. In order to provide pH control, which consequently affects drug stability, Esomeprazole batches, produced in the same way, were kept in partially closed vials for 3 h at temperatures of 20 °C and −30 °C, after which they were lyophilized and stored for long-term stability for 36 months. The aim of the presented study was to apply a deep-learning algorithm for the prediction of the Esomeprazole stability profile and to determine the pH limit for the reconstituted solution of the final freeze-dried product that would assure a quality product profile over a storage period of 36 months. Multilayer perceptron (MLP) as a deep learning tool, with four layers, was used. The pH value of Esomeprazole solution and time of storage (months) were inputs for the network, while Esomeprazole assay and four main impurities were outputs of the network. In order to keep all related substances and Esomeprazole assay in accordance with specifications for the whole shelf life, the pH value for the reconstituted finish product should be set in the range of 10.4–10.6.