Pain on vaccine injection and subsequent site reactions of pain and swelling may influence confidence in vaccines and their uptake. This study aimed to identify factors associated with reported pain on injection and reactogenicity following administration of a strain specific meningococcal B outer membrane vesicle vaccine. A retrospective analysis of data was conducted from a phase II single center randomized observer-blind study that evaluated the safety, reactogenicity and immunogenicity of this vaccine in two cohorts of healthy eight to 12 year old children. Vaccine administration technique was observed by an unblinded team member and the vaccine administrator instructed on standardized administration. Participants kept a daily diary to record local reactions (erythema, induration and swelling) and pain for seven days following receipt of the vaccine. Explanatory variables were cohort, vaccine, age, gender, ethnicity, body mass index, atopic history, history of frequent infections, history of drug reactions, pain on injection, vaccinator, school population socioeconomic status, serum bactericidal antibody titer against the vaccine strain NZ98/254, and total IgG. Univariate and multivariable analyses were conducted using ordinal logistic regression for factors relating to pain on injection and reactogenicity. Perceived pain on injection was related to vaccine formulation, vaccine administrator and ethnicity. Reactogenicity outcomes varied with ethnicity and vaccine administrator. Maintaining community and parental confidence in vaccine safety without drawing attention to differences between individuals and groups is likely to become increasingly difficult. Vaccine administration technique alone has the potential to significantly reduce pain experienced on injection and local vaccine reactions.