Photopharmacology is a field of medicine and pharmacology that uses light to selectively activate or deactivate pharmaceutical agents. This approach significantly enhances and localizes the drug action and, therefore, reduces its side effects. Apart from the bioactive moiety, any photopharmacological compound should contain a photoactive group that must absorb light at the desired wavelength and reorganize the molecular structure after photoactivation. The design of an effective photopharmacological compound requires careful tuning of physical, chemical, and biological properties. The present review summarizes and analyzes the main approaches to the molecular design of photopharmacological drugs based on azobenzene or azoheteroarenes. The main ideas and methods used for tuning spectral and photochemical properties of compounds of this class are discussed. A comparative analysis of main computational methods for their in silico screening is carried out; the most common approaches to the synthesis of azobenzenes and azoheteroarenes derivatives are systematized. Special attention is given to the methods and approaches that are specific to the molecular design of photopharmacological compounds with required physicochemical and photochemical properties.