Introduction Rabies remains a global threat, with annually over 59,000 deaths. Intradermal (ID) pre-exposure prophylaxis (PrEP) is very efficient and reduces the need for rabies immunoglobulins. Not much is known about factors that influence the immune response to ID administered rabies vaccine. The aim of this study is to determine if variations in timing of vaccine administration and serology determination, age and gender have an influence on the levels of rabies virus neutralizing antibody (RVNA) after ID rabies vaccination. Materials and Methods This is a retrospective study based on electronic health record vaccination data of Belgian military personnel who received ID rabies PrEP with a three injections regimen during the period 2014–2017. Serology was determined by using the RFFIT method. Fischer’s exacts tests were used to evaluate the effect of each independent variable on RVNA levels. Results In this study, 2,112 subjects were included. All but one seroconverted with a RVNA level ≥0.5 IU/mL. About 48% of subjects developed an antibody titer of >10 IU/mL, 36% had antibody levels 3–10 IU/mL and 16% had an antibody level 0.5–2.99 IU/mL. Statistically significant (p = 0.0018) higher RVNA levels are observed in the groups that received vaccination doses later as planned. Timing of serology determination also influenced RVNA levels significantly (p = 0.000). Antibody levels were significantly higher in females than in males (p = 0.000). Age did influence RVNA levels significantly (p = 0.022). Conclusions Timing of vaccine dose administration, timing of serology testing, sex and age do significantly influence the humoral B-cell response to ID administered rabies vaccine.