Zika and chikungunya viruses have caused major epidemics and are transmitted by Aedes aegypti and/or Aedes albopictus mosquitoes. The ‘Sementis Copenhagen Vector’ (SCV) system is a recently developed vaccinia-based, multiplication-defective, vaccine vector technology that allows manufacture in modified CHO cells. Herein we describe a single vector construct SCV vaccine that encodes the structural polyprotein cassettes of both Zika and chikungunya viruses from different loci. A single prophylactic vaccination of mice induces neutralizing antibodies to both viruses in wild-type and IFNAR-/- mice and protects against (i) chikungunya virus viremia and arthritis in wild-type mice, (ii) Zika virus viremia and fetal/placental infection in female IFNAR-/- mice and (iii) Zika virus viremia and testes infection and pathology in male IFNAR-/- mice. To our knowledge this represents the first single vector construct, multi-pathogen vaccine encoding large polyproteins, and offers both simplified manufacturing and formulation, and reduced “shot burden” for these often co-circulating arboviruses. However, Zika virus is known to persist in male testis. The current work evaluates a therapeutic vaccination approach to reduce viral load in the testis following Zika infection. In summary, we have produced a novel platform technology that can readily be accommodated in a biopharmaceutical industry-standard manufacturing process. A single vector targeting multiple diseases is an innovative approach to reducing “shot burden” for commonly co-circulating viruses.