Closing the yield gap of strategic crops can facilitate achieving sustainable solutions to alleviate hunger, ensure food security, and enhance nutrition. This study aimed to quantify factors affecting rice yield gap in northern Iran using experimental and survey data on yields and management practices. The CERES-Rice model, calibrated with data (2011, 2016, 2019) from two regions, was used to estimate potential yield (Yp) of different rice cultivars. Yield gaps were calculated as the difference between economic yield potential and the average yield attained by farmers. The calibration process showed that cultivar coefficients varied across rice varieties. The simulated yields (2012–2021) showed that the mean potential yields were 13362 kg ha−1 and 8818 kg ha−1 for the late and early-maturing cultivars, respectively. High temperature was the most important yield defining factor across the rice growing areas. The yield gap was 3751 kg ha−1 and 2830 kg ha−1 in the late- and early-maturing cultivars, respectively. Nitrogen fertilizer rate, number of fertilizer applications, phosphorus fertilizer rate, transplanting date, potassium fertilizer rate, and seedling age were the top factors influencing the yield gap. Among the management factors, rice fertilizer management explained about 65% of the yield variability. Together, transplanting date and seedling age explained 15.3% of the variability in rice production, while pest, disease, and weed damage accounted for 9.6%. Breaking down the yield gap into affecting factors allows growers to improve the production system by providing the best crop management according to their facilities and capabilities. This approach is essential for optimizing agricultural productivity and achieving sustainable food production goals.