Malate dehydrogenase (MDH) (EC 1.1.1.40) is among the major genes identified by the C₄ Rice Consortium to play an important part in inducing C₄ photosynthesis in a C₃ rice system. Despite the vast information on the biochemical characteristics of the enzyme, the effects of engineering maize (Zea mays L.) MDH on IR64 rice (Oryza sativa L.) for the induction of the C₄ pathway was never thoroughly studied in the light of transcriptomics. Two transformed IR64 rice events conferring overexpression of maize MDH (ZmMDH), namely MDH22 and MDH48, were analyzed using transcriptome analyses to assess differential expression of endogenous genes due to MDH overexpression. Sugar metabolite quantification was also conducted to identify changes in the concentration of simple and complex carbohydrates against the wild type (untransformed) IR64 rice. Transcriptome analyses revealed 301 differentially expressed genes in transformed rice with significant enriched effects in the downregulation of simple carbohydrate degradation. This result implies lower degradation of sucrose, fructose and glucose content as eight strongly associated genes for this function were downregulated. Carbohydrate characterization revealed significant differences in terms of simple and complex sugar content in MDH22 and MDH48, respectively, which aligned with the results of the transcriptome analyses. The resulting phenotype of the MDH-transformed lines indicate an increase in plant height and biomass which can be attributed to the association of growth due to the rapid conversion of simple sugars to starch and traced further to the implied change in the rate of simple sugar degradation. The study successfully established the effect of maize MDH in rice based on its transcriptome, sugar content, and phenotype.