The dataset presented here are part of the data planned to produce biodiesel from flaxseed. Biodiesel production from flaxseed oil through transesterification process using KOH as catalyst, and the operating parameters were optimized with the help of face-centered central composite design (FCCD) of response surface methodology (RSM). The operating independent variables selected such as, methanol oil ratio (4:1 to 6:1), catalyst (KOH) weight (0.40–1.0%), temperature (35 °C–65 °C), and reaction time (30 min–60 min) were optimized against biodiesel yield as response. The maximum yield (98.6%) of biodiesel from flaxseed can achieved at optimum methanol oil ratio (5.9:1), catalyst (KOH) weight (0.51%), reaction temperature (59.2 °C), and reaction time (33 min). The statistical significance of the data set was tested through the analysis of variance (ANOVA). These data were the part of the results reported in “Optimization of process variables for biodiesel production by transesterification of flaxseed oil and produced biodiesel characterizations” Renewable Energy .