Cancer is one of the most common families of diseases today with millions of new patients every year around the world. Bladder cancer (BC) is one of the most prevalent types of cancer affecting both genders, and it is not known to be associated with a specific group in the population. The current treatment standard for BC follows a standard weekly Bacillus Calmette–Guérin (BCG) immunotherapy-based therapy protocol which includes BCG and IL-2 injections. Unfortunately, due to the biological and clinical complexity of the interactions between the immune system, treatment, and cancer cells, clinical outcomes vary significantly among patients. Unfortunately, existing models are commonly developed for a non-existing average patient or pose strict, unrealistic, expectations on the treatment process. In this work, we propose the most extensive ordinary differential equation-based biological model of BCG treatment to date and a deep learning-based scheduling approach to obtain a personalized treatment schedule. Our results show that resulting treatment schedules favorably compare with the current standard practices and the current state-of-the-art scheduling approach.