Rural structural transformation is best defined as structural changes in the rural areas occasioned by government policies and programmes with the intention of altering the contributions of major sector of the economy for the enhancement of agricultural sector. The study aimed at investigating the impact of rural structural transformation on agricultural productivity in Nigeria. The methodology adopted for the study was Structural Autoregression (SVAR). Six variables of expenditure on education (EXPE), expenditure on health (EXPH), expenditure on electricity (EXPEL), expenditure on telecommunication (EXPTC), expenditure on roads and construction (EXPRC) and expenditure on agriculture (EXPA). Of the six explanatory variables only expenditure on agriculture was found to be negatively related to agricultural productivity, while the others were positively related to it. Several reasons of which of official corruption by the handlers of agricultural funds could possibly be one of the reasons for the negative relationship between expenditure on agriculture and agricultural productivity. Among many other recommendations was the need to provide clinics and health centres to the rural areas, provision of good and accessible roads, provision of electricity and internet facilities. This will act as motivating factors in curbing rural-urban migration, and by extension improve the lots of agricultural productivity in Nigeria. Keywords: rural, structural transformation, agricultural productivity, agricultural policies and structural VAR