Long COVID, an umbrella term referring to a variety of symptoms and clinical presentations that emerges in a subset of patients after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has a significant effect on quality of life and places a substantial burden on health care systems worldwide, straining financial and human resources. The pathophysiology of long COVID remains incompletely understood, though several hypotheses have been proposed to explain different aspects of this complex condition. SARS-CoV-2 persistence, direct organ damage, innate and adaptive immune system perturbation, autoimmunity, latent virus reactivation, endothelial dysfunction, and microbiome disturbances are among the most relevant avenues for elucidating the evolution, complexity, and mechanisms of long COVID. Active investigation regarding potential biomarkers for long COVID and its associated disease endotypes highlights the role of inflammatory mediators, immunophenotyping, and multiomics approaches. Further advances in understanding long COVID are needed to inform current and future therapeutics.