Campylobacter is the leading bacterial cause of human enteritis in developed countries. Chicken is a major natural host of Campylobacter. Thus, on-farm control of Campylobacter load in poultry would reduce the risk of human exposure to this pathogen. Vaccination is an attractive intervention measure to mitigate Campylobacter in poultry. Our previous studies have demonstrated that Campylobacter outer membrane proteins CmeC (a component of multidrug efflux pump) and CfrA (ferric enterobactin receptor) are feasible and promising candidates for vaccine development. In this study, by targeting these two attractive vaccine candidates, we explored and evaluated a new vaccination strategy, which combines the in ovo vaccination route and novel DNA vaccine formulation, for Campylobacter control in broilers. We observed that direct cloning of cfrA or cmeC gene into the eukaryotic expression vector pCAGGS did not lead to sufficient level of production of the target proteins in the eukaryotic HEK-293 cell line. However, introduction of the Kozak consensus sequence (ACCATGG) in the cloned bacterial genes greatly enhanced production of inserted gene in eukaryotic cells, creating desired DNA vaccines. Subsequently, the validated DNA vaccines were prepared and used for two independent in ovo vaccination trials to evaluate their immune response and protective efficacy. However, single in ovo injection of specific DNA vaccine at 18th day of embryonation, regardless using neutral lipid-protected vector or not, failed to trigger significant IgG and IgA immune responses and did not confer protection against C. jejuni colonization in the intestine of chickens. In conclusion, this study demonstrates that the Kozak sequence is critically important for construction of the DNA vaccine expressing prokaryotic gene. The optimal regimen for in ovo vaccination of DNA vaccine for Campylobacter control in poultry needs to be determined in future studies.