Monsoon fluctuations have a reflective influence on rice productivity, which is the main foodgrain in India. The impact of El Niño on spatial variability of summer monsoon rainfall and thereby kharif rice productivity was analysed for the period 1974–2009. It was clear from the analysis that the delayed onset of monsoon along with El Niño has varied influences on rice productivity over different rice growing states as well as over India. Out of eight El Niño years, 6 years received deficit rainfall during monsoon season. But, the quantity of deficit varies from −20.3% in 2002 to −5.5% in 1991. The monthly distribution of monsoon rainfall shows higher frequency of deficit occurred during July and September. Interestingly, all El Niño years, except in 1997, September received deficit in rainfall which indicate the early withdrawal of monsoon. During 8 moderate and strong El Niño years, 5 years the kharif rice productivity falls below the technological trend ranging by between −4.3% in 1986 and −13.8% in 2002 over India. There exists a wide spatial variability of normalized kharif rice productivity anomaly during moderate El Niño event, with a maximum of −21.9% over Gujarat followed by −15.9% at Maharashtra. However, during the strong El Niño event, there is a maximum of −14.2% at Bihar to −6.6% over Maharashtra. The correlation between normalized monthly rainfall anomaly and rice productivity anomaly during the El Niño years indicated that July rainfall contributed 71% of the variations in rice productivity. Analysis of El Niño impact on spatial rice productivity may be useful for formulating farm-level site specific management planning and policy decisions.