Lignocellulosic biomass is still being looked into as a feasible source of bioethanol production. The yeast Saccharomyces cerevisiae can adapt to in situ detoxify lignocellulose-derived inhibitors, including furfural. Tolerance of strain performance has been measured by the length of the lag phase for cell growth in response to the challenge of the inhibitors. The aim of this work was to obtain a yeast-tolerant strain of YPR015C against furfural through overexpression using the in vivo homologous recombination method. The overexpressed yeast strain displayed much better resistance to furfural than its parental strain. Comparative transcriptomic analysis revealed 79 genes potentially involved in amino acid biosynthesis, oxidative stress, cell wall response, heat shock protein and mitochondrial associated protein for the YPR015C overexpression strain associated with stress responses to furfural at the late stage of lag phase growth. Fluorescence microscopy revealed improved enzyme reductase activity, accumulation of reactive species and cell wall susceptibility to the harmful effects of furfural inhibitor in contrast to its parental strain. Both up- and down-regulated genes involved in diversified functional categories were accountable for tolerance in yeast to survive and adapt the furfural stress in a time course study during the lag phase growth