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In order to investigate the origin of matter-antimatter asymmetry in the Universe, we adopt a theoretical framework where the standard model emerges as a Poincaré invariant field theory localized at a domain-antidomain wall (DW-aDW) brane pair of a theory which lives on a higher dimensional bulk. We argue that such a system of a parallel DW-aDW pair could have been created at a very early epoch of the cosmological evolution when the Universe was still of microscopic size because its creation is topologically possible as compared to a single DW creation when the perpendicular extra dimension is compact. The conservation laws, such as of charge and chirality, are not violated in vacuum fluctuations of the combined DW-aDW system, but as we show their simultaneous conservation for each wall separately may not be favorable in certain processes. In particular, as expansion of spacetime occurs in the higher dimensional bulk, the distance d between the DW and the aDW increases as a function of time. We show that during the early stages of the cosmological evolution, when d was of microscopic size, the leading mechanism for pair-creation from fluctuations of the gauge-field with polarization perpendicular to the DWs (i.e., polarization along the extra dimension) was one in which the particle and the antiparticle were created on the opposite domain-walls hosting opposite chirality fermions. This mechanism allows for a matter-antimatter asymmetry to appear separately in the DW and the aDW, while in the combined DW-aDW system no such asymmetry was allowed. In this scenario, at a later and the present stage of the cosmological evolution, where d is macroscopically large, the probability to violate these conservation laws on a single DW, as a function of the inter-wall distance, is exponentially suppressed.