Elevated morbidity and mortality rates associated with mucosal infections have become alarming globally. Recently, the SARS-CoV-2 pandemic has portrayed some harsh images of respiratory mucosal infections all over the world. The existence of nonspecific suboptimal mucosal vaccines against COVID-19 critically presents challenges to managing and saving the lives of those who suffer. The mammalian mucosal immune system contains a typical system of cellular tissues and soluble molecular components that performs a defense mechanism against invaders (pathogens) and malignant cells. Mucosal nanovaccines have emerged as a prospective first-line of defense approach for devastating pathogens by eliciting both site-specific and systemic immunity or responses. Mucosal nanovaccines not only check pathogenic infections at the mucosal site, and boost immunogenicity but also combat associated systemic disorders precisely due to their superior surface area, augmented bioavailability, enriched antigen-invading cell environment at the mucosal site, and thus shield the entry portal (oral and nasal) for antigens. Mucosal immunization elicits promising immunomodulation by turning up and down proteins involved in certain allergies and autoimmune disorders. This chapter outlines different types of mucosal immune responses and advanced applications of nanovaccines developed by polymeric nanoparticles, carbon nanotubes, inorganic particles, and virus-like biomimetic particles against pathogenic infections, autoimmune mucosal disorders, and so they can aid in chemotherapy and prophylactics as well.