The examined the effect of structural adjustment programme on the performance of small and medium scale enterprises in Nigeria. The research design adopted for the study is ex-post facto and the population of this is all the small and medium scale enterprises in Nigeria. The population of the study is 72838 and was used as the sample size. Structural adjustment programme was measured by import substitution policy and export promotion policy and small and medium scale enterprise performance was measured by SMEs output. The study covered a period of 32 years from 1986-2017. The statistical tools adopted in this study were descriptive statistics, correlation analysis, unit root test and Regression. The analysis was conducted using e-view statistical software and the finding indicates that there was a negative and significant effect relationship between structural adjustment programme and performance of Small and medium scale enterprises in Nigeria. The study also found that LIM has a positive and significant effect on LSMEOPT in Nigeria. Also, LEX has a negative and significant effect on LSMEOPT in Nigeria. The study suggested that Government in Nigeria should reduced the adoption of SAP in Nigeria but should only embark on import substitution since before the adoption of SAP, Nigerian introduced indigenization policy in 1977. Government of Nigeria should designed policy that discourage the people of Nigeria to purchase SMEs manufactured products from the richer countries. They should only sell their primary products on the world market, but their foreign exchange reserves should not be used to purchase the manufactures products from abroad.