Lysimetric and eddy covariance techniques are commonly used to directly estimate actual crop evapotranspiration (ETa). However, these technologies are costly, laborious, and require skills which make in situ ET estimation difficult, particularly in developing countries. With this in mind, an attempt was made to determine ETa and stagewise crop coefficient (Kc) values of transplanted puddled rice using a modified non-weighing paddy lysimeter. The results were compared to indirect methods, viz., FAO Penman–Monteith and pan evaporation. Daily ETa ranged from 1.9 to 8.2 mmday−1, with a mean of 4.02 ± 1.35 mmday−1, and their comparison showed that the FAO Penman–Monteith equation performed well for the coefficient of determination (R2 of 0.63), root mean squared error (RMSE = 0.80), and mean absolute percentage error (MAPE = 13.6 %), and was highly correlated with ETa throughout the crop season. However, the pan evaporation approach was underestimated (R2 of 0.24; RMSE = 0.98; MAPE = 22.13%) due to a consistent pan coefficient value (0.71), vegetation role and measurement errors. In addition, actual Kc values were obtained as 1.13 ± 0.13, 1.27 ± 0.2, 1.23 ± 0.16, and 0.93 ± 0.18 for the initial, crop development, mid-season, and end-season stages, respectively. These estimated crop coefficient values were higher than FAO Kc values. Statistical analysis results revealed that the overall stagewise-derived average Kc values were in line with FAO values, but different from the derived pan Kc values, although found insignificant at a 5% significance level. In addition, water productivity and agro-meteorological indices were derived to evaluate the cultivar performance in this experiment. Therefore, such a methodology may be used in the absence of weighing lysimeter-derived Kc values. The derived regional Kc values can be applied to improve irrigation scheduling under similar agro-climatic conditions.