Rice serves as a source of livelihood to millions of people as staple food. Stem rot of rice caused by Sclerotium oryzae has been an agriculturally significant disease cause about 35% of crop loss. This review dealt with stem rot management strategies applying various agronomic practices. Control of stem rot using fungicide leads to environmental hazour along with its residual effect on human health. Thus, biocontrol using Trichoderma is an alternative cost effective method. Utilization of resistant wild rice genotypes like Oryza rufipogon, O. spontanea and O. nivara opens scope for safe transmission of the heritable trait through breeding. Plant immunisation by undderstanding pathogen associated molecular patterns (PAMPs), molecular interaction between the elicitors and the corresponding plant receptor protein, R-gene-dependent resistance, host specific resistance by defense signaling through conserve nucleotide-binding and leucine-rich repeat domains are discussed. Early defense response (EDR), role of ROS, anti-oxidant enzymes, plant specific phytoalexin synthesis, release of defense signaling molecules, activation of different signaling pathways are also presented on plant defiance strategy. Activation of MAPKs, npr1 gene regulation, abundant expression of transcript factors (TF) genes, anti-microbial PR protein release, systemic acquired resistance by metal ions induced proteins may be utilized applying biotechnological tools for acquiring stem rot resistance in rice. •This review dealt with stem rot management of rice caused by Sclerotium oryzae and molecular mechanism of disease resistance.•Synthetic elicitors and low dose cadmium induced proteins (~43 kDa or ~47 kDa) are important precursor imparting resistance.•Receptor protein interactions, R-gene expression and defense signaling through conserve nucleotide-binding are discussed.•Role of ROS, anti-oxidants, phytoalexin synthesis, activation of signaling pathways as defence response are presented.•Transfer of MAPKs, npr1 and metal induced gens into the sensitive varieties in developing stem tor resistant rice is safer.