Filamentous hemagglutinin (FHA), a major virulence factor of classical Bordetellae, is a rod-shaped molecule that plays an important role in the adherence of bacteria to ciliated epithelial cells of the upper respiratory tract and suppresses the host innate and adaptive immune response. FHA is translated as a 360-kDa FhaB precursor that is exported across the outer bacterial membrane by a two-partner secretion mechanism involving the outer membrane protein FhaC and shed into external environment as an N-terminal ‘mature’ 220-kDa FHA protein after processing by surface-exposed SphB1 protease. The remaining C-terminal 130-kDa FhaB prodomain is thought to regulate maturation process and rapidly degraded in the periplasm. We show here that both the extreme C terminus (ECT) of the FhaB prodomain and the mature FHA play the pivotal roles in the virulence of B. pertussis. The NMR-based structural analysis of ECT, a highly-conserved the C-terminal 100 residues of the FhaB precursor, revealed that the ECT polypeptide adopts a rigid structure with a ‘pilin-like’ protein fold. Deletion of the sequence encoding ECT (ΔECT) resulted in a significant decrease in bacterial colonization within the nasal cavity of infected mice, comparable to B. pertussis strain lacking the FhaB precursor (ΔFhaB). Intriguingly, the ΔECT strain exhibited a complete loss of its ability to bind cilia on human nasal epithelial cells grown at the air-liquid interface, emphasizing the indispensable role of ECT in the adherence of Bordetella cells to ciliated epithelial cells. Furthermore, we demonstrate the mature FHA confers resistance of B. pertussis to complement-mediated killing, highlighting its involvement in protection of bacterial cells against the host’s innate immune response. Collectively, these results provide novel insights into FHA biology, unraveling its multifaceted role in the virulence of pathogenic Bordetellae.