Mycoplasma pneumoniae (Mp) is carried in the upper respiratory tract (URT) of mice after symptomatic infection. B cells and Mp-specific antibodies are crucial for Mp clearance in the lungs of mice but are limited in clearing Mp from the URT. Abstract Background Carriage of Mycoplasma pneumoniae (Mp) in the nasopharynx is considered a prerequisite for pulmonary infection. It is interesting to note that Mp carriage is also detected after infection. Although B cells are known to be involved in pulmonary Mp clearance, their role in Mp carriage is unknown. Methods In this study, we show in a mouse model that Mp persists in the nose after pulmonary infection, similar to humans. Results Infection of mice enhanced Mp-specific immunoglobulin (Ig) M and IgG levels in serum and bronchoalveolar lavage fluid. However, nasal washes only contained elevated Mp-specific IgA. These differences in Ig compartmentalization correlated with differences in Mp-specific B cell responses between nose- and lung-draining lymphoid tissues. Moreover, transferred Mp-specific serum Igs had no effect on nasal carriage in B cell-deficient μMT mice, whereas this enabled μMT mice to clear pulmonary Mp infection. Conclusions We report the first evidence that humoral immunity is limited in clearing Mp from the upper respiratory tract.