Due to its subtropical origin, rice (Oryza sativa L.) is sensitive to low-temperature stress. We report the identification of LOC_Os04g24110, annotated to encode the UDP-glycosyltransferase enzyme UGT90A1, as a gene associated with the low-temperature seedling survivability (LTSS) quantitative trait locus qLTSS4-1. Haplotype differences in the control region of OsUGT90A1 affecting differential expression in chilling tolerant and chilling sensitive rice accessions rather than differences in protein sequences correlate with chilling tolerance phenotypes. OsUGT90A1 expression is cold regulated, and its overexpression helps to maintain membrane integrity during cold stress and promotes leaf growth during stress recovery, correlating with reduced levels of reactive oxygen species due to increased antioxidant enzyme activities. Overexpression of OsUGT90A1 in Arabidopsis moreover improves freezing survival and salt stress tolerance, correlating with enhanced antioxidant enzyme activities. In rice, overexpression of OsUGT90A1 decreases while gene knockout increases root lengths of three-week-old seedlings, indicating that differential expression of this gene may affect phytohormone activities. Thus, higher OsUGT90A1 expression in chilling tolerant than chilling sensitive accessions helps maintain cell membrane integrity as an abiotic stress tolerance response mechanism to prepare plants to resume growth and development during stress recovery.