Confined systems exhibit a large variety of nonequilibrium phenomena. In this special issue, we have collected a limited number of papers that were presented during the XXV Sitges Conference on Statistical Mechanics, devoted to "Nonequilibrium phenomena in confined systems". The conference took place in Barcelona from the 6th until the 10th of June 2016 (http://www.ffn.ub.es/~sitges25/), was organized by G. Franzese, I. Latella, D. Reguera, and J.M. Rubi, and gathered more than 60 international scientists in the areas of physics, chemistry, and biology working on confined systems in topics like: Diffusion and entropic transport in confined systems; Ion and polymer translocation; Phase transitions and chemical reactions in confined media; Forces induced by fluctuations in confined systems and Casimir effect; Confined active matter; Macromolecular crowding; and Energy conversion in confinement.