Sugarcane is an essential commodity in Indonesia. However, climate change negatively affects the sugarcane production efficiency. This study aims to measure the technical efficiency of sugarcane farming using a bootstrap data envelopment analysis (DEA) approach, compare the efficiency of irrigated and rain-fed sugarcane farming, and determine the factors affecting the technical efficiency of sugarcane farming in East Java, Indonesia. Primary data were collected from 451 sugarcane farmers during the 2020–2021 planting season. The results indicate that the “bias-corrected” technical efficiency scores of the single- and double-bootstrap approach (0.624 and 0.561) were lower than that of conventional DEA (0.714). The efficiency score of irrigated sugarcane farms (0.593) was higher than that of rain-fed farms (0.529). Moreover, the farmers’ age, household size, dependency, farming experience, training, subsidies, crop diversification, and access to irrigation impacted sugarcane farming’s technical efficiency. Improvement of 1% in training, irrigation access, and subsidies increased the technical efficiency by 0.034, 0.032, and 0.030, respectively. This strategy is expected to enhance the productivity and technical efficiency and reduce the poverty in rural households in East Java.