Bordetella pertussis causes whooping cough. The predominant strains in Australia changed to single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele ptxP3/pertactin gene allele prn2) from SNP cluster II (non-ptxP3/non-prn2). SNP Cluster I was mostly responsible for the 2008–2012 Australian epidemic. Our previous proteomic analysis identified potential proteomic adaptations in the whole cell and secretome of SNP cluster I. Additionally, current ACVs were shown to be less efficacious against SNP cluster I in mice models and there is a pressing need to discover new antigens to improve the ACV. One important source of novel antigens is the surfaceome. Therefore, this study established surface shaving in B. pertussis to compare the surfaceome of SNP cluster I (L1423) and II (L1191), and identify novel surface antigens for vaccine development. Surface shaving using 1 μg of trypsin for 5 min identified 126 proteins from 666 peptides detected with the most abundant being virulence-associated and known outer membrane proteins. Cell viability counts showed minimal lysis from shaving. The proportion of immunogenic proteins was higher in the surfaceome than in the whole cell and secretome. Of the 126 proteins, 6 were unique to L1423 including two transport proteins and 2 were unique to L1191, both of which are known to be immunogenic. Two type III secretion system proteins also known to be immunogenic were downregulated in L1423, providing further evidence of proteomic adaptation in SNP cluster I. Finally, a comparison of proteins in each sub-proteome identified 22 common proteins. These included 11 virulence proteins and 11 housekeeping proteins which were immunogenic, essential and consistently expressed thus demonstrating their potential as future targets. This study established surface saving in B. pertussis and identified unknown surface proteins which may be potential vaccine antigens.