Abstract The development of e-commerce requires the strengthening of this component of the pharmaceutical business while providing the population with medicines. Improving the operation of pharmacy websites is an important task with a significant marketing effect. The purpose of the study is to identify errors on pharmacy websites that worsen their usability and communicative qualities when interacting with visitors, to offer an approach based on a joint assessment of consumer perception and technical parameters, and to carry out calculations for a comparative analysis of such sites functional and technical components using a multi-criteria approach. The objectives of the study were to analyze the Internet trade in medicines, to determine the criteria for comparison of pharmacy sites, to develop a model for website evaluation, and to analyze the results of site quality estimation. Multicriteria comparison with different importance of criteria was used as the methodology to evaluate the usability of sites for online buyers of pharmaceutical products. As result two main components of the quality of pharmacy sites are identified: user interface and technical characteristics. The parameters of site evaluation for these components are described, and evaluation is performed. A computer model in Excel has been developed. The proposed approach and the program allow for assessing pharmacy sites’ quality, comparing their marketing opportunities, directions to improve functionality, pharmaceutical services, and business position of pharmacies. The described steps for website estimations can be used not only in pharmaceutical services but for wide kinds of sites for e-commerce.