The study investigated empirically the effect of banking sector reforms on the output of manufacturing sector in the Nigerian economy between 1970 and 2011 with a view to examining the extent of the impact of banking sector reforms on the manufacturing sector. The study employed annual secondary time series data from 1970-2011, sourced from the Central Bank of Nigeria's statistical bulletin and annual report and statement of accounts, National Bureau of Statistics final accounts and IMF International Financial Statistics (IFS) using the methodology of Cointegration analysis and Error Correction Mechanism (ECM). The empirical results showed that the effects of Bank assets, Lending rate, Exchange rate and real rate of interest on manufacturing output were positively significant but with very low impact. On the other hand, the financial deepening and interest rate spread negatively and significantly impacted on the output growth of manufacturing sector in Nigeria. Overall, the conclusion that emerged from the findings suggests that the effects of banking sector reforms on the output growth of manufacturing sector were significantly low in the Nigerian economy. However, the findings indicated that the impacts of the various banking reforms could vary widely on the economy depending on the time lags involved. Consequently, the policymakers must be prepared to initiate proper countercyclical banking reforms that will serve as buffer measures to lessen or abort the negative impacts of any banking reforms on the manufacturing output growth. Thus a flexible accommodating banking reform regime is advocated for Nigeria.