Submergence 1A (SUB1A), is an ethylene response factor (ERF) that confers submergence tolerance in rice via limiting shoot elongation during inundation period. SUB1A has been proposed to restrict shoot growth by modulating gibberellic acid (GA) signaling. Our transcriptome analysis indicated that SUB1A differentially regulates genes associated with brassinosteroid (BR) synthesis during submergence. Consistent with the gene expression data, the SUB1A genotype had higher brassinosteroid levels after submergence compared to the intolerant genotype. Tolerance to submergence can be activated in the intolerant genotype by pretreatment with exogenous brassinolide, which results in restricted shoot elongation during submergence. BR induced a GA catabolic gene, resulting in reduced GA levels in SUB1A plants. BR treatment also induced the DELLA protein SLR1, a known repressor of GA responses such as shoot elongation. We propose that BR limits GA levels during submergence in the SUB1A rice through a GA catabolic enzyme as part of an early response and may repress GA responses by inducing SLR1 after several days of submergence. Our results suggest that BR biosynthesis is regulated in a SUB1A-dependent manner during submergence and is involved in modulating the GA signaling and homeostasis.