Streptococcus pneumoniae is comprised of more than 90 serotypes and is the major causative agent of pneumonia, which results in over 1 million deaths worldwide every year. Currently available injectable vaccines can protect against only 13–23 serotypes, and result in decrease of colonization against vaccine serotypes. However, they are neither effective for inhibition of non-vaccine serotypes colonization nor inhibition against initial colonization in the nasopharynx against various serotypes. Thus, development of a vaccine conveying broader protection at the colonization stage is required. This study examined whether the Δpep27 mutant could provide protection at the nasopharynx against a broad range of serotypes. Δpep27 immunization stimulated secretion of IL-4, IL-10, TNF-α, INF-γ and IL-17, and significantly increased secretory-IgA levels in bronchoalveolar lavage fluid. Colonization and opsonophagocytosis assays demonstrated that Δpep27 immunization could protect against many heterologous infections, including non-typeable strains, at the nasopharynx, and prompted efficient killing of heterologous strains, suggesting that Δpep27 immunization provides a wide range of cross-protection. Furthermore, Δpep27 immunization significantly increased both the survival rate and the level of IgG 3 months post-immunization, demonstrating long-lasting immunity. Thus, Δpep27 could serve as a highly feasible mucosal vaccine once it is further developed into a non-transformable strain.