Rice production holds a significant position in the Thai economy. Although it is the world’s largest rice exporter, Thailand’s increase in rice production is the result of an expansion in the cultivation area rather than an increase in yield per unit area. The present study was designed to estimate the technical efficiency and its governing factors for certified organic rice-growing farms in Yasothon Province, Thailand. A data envelopment model was employed to assess the technical efficiency of 328 farmer groups. The data revealed that the average technical efficiency was 23% and 28% under constant returns to scale (CRS) and variable returns to scale (VRS) specifications, respectively. Farmers can reduce the use of machinery, fertilizer, seed, and labor as input factors by about 80.1%, 25.62%, 24.72%, and 19.15%, respectively, while still achieving the same level of output. Multiple regression analysis was applied to estimate factors that affect the pure technical efficiency score (PTES) in the test regions. Results show that household size, farm size, water source, market accessibility, health symptoms, income, and labor were highly related to the TES and the amount of organic rice production. The regression coefficients of the predictors show that the income was the best predictor of the PTES at a significance level of p < 0.05. It is concluded that the farmers can potentially increase their yields by up to 72%–77% under current management practices.