Background Proof of effects of Cytosine Phosphoguanine Oligodeoxynucleotides (CpG ODNs), adjuvanted Hepatitis B Virus (HBV) vaccine on immune response is limited. This study aimed to assess the effect of five CpG ODNs in HBV Vaccine-immunized BALB/c mice and to identify the most effective CpG ODN adjuvant. Methods This laboratory-based experimental study was conducted using a total of 36 female BALB/c mice, which were clustered into 12 groups and immunized intramuscularly. Group 1 was immunized with CpG ODN 18281-1 alone, group 2 with vaccine plus CpG ODN 18281-1, group 3 with CpG ODN 18281-2 alone, group 4 with CpG ODN 18281-2 plus vaccine, group 5 CpG ODN 18289 alone, group 6 with CpG ODN 18289 plus vaccine, group 7 CpG ODN 1826 S alone, group 8 with CpG ODN 1826 S plus vaccine, group 9 CpG ODN 2395 alone, group 10 with CpG ODN 2395 plus vaccine, group 11 with vaccine alone and group 12 with Phosphate Buffer Saline (PBS). All the groups were observed for 14 and 28 days after immunization. Results In the vaccinated groups, those receiving supplementation with CpG 2395 exhibited a significant 4.4-fold elevation, resulting in a signal-to-noise ratio (S/N) value of 14.1 compared to the vaccine group only (S/N = 3.22) by day 28 (p-value < 0.0001). For mice immunized with the vaccine plus CpG ODNs, cytokine profiling using real-time quantitative polymerase chain reaction revealed increased IL-6 expression levels and decreased TNF-α levels compared to the untreated group, normalized with the housekeeping gene HPRT 1. However, the expression of IL-6 and TNF-α was not statistically significant between the treated groups (p-value ≥ 0.2). Parameters for toxicity were within the normal range in all treatment groups. Conclusion Based on these results the co-administration of the HBV vaccine with CpG ODN 2395 induces high immune responses in comparison to HBV vaccine alone.