Climate fluctuation is foretold to have unfavourable impact on the agriculture of the poorer parts of the world, especially the developing countries like Nigeria. In Nigeria, crop productions are mostly low-technology based, and therefore seriously sensitive to environmental factors. Climate variability is setting Nigeria's agricultural system under unspeakable stress and threat. Research on the impact of climate variability on agricultural outputs is necessary because of its effects in changing standards of living trends in the nation. Descriptive statistics (tables) and co-integration analysis are the methods used to analyze the data explored in this research. The findings demonstrate that the rate of agricultural output (maize and rice) is fluctuating from 1971 to 2009. There were changes in the patterns of rainfall and relative humidity. Sunshine and temperature were not consistently steady also. The results indicate that all variables were stationary at their level. When the Augmented Dickey-Fuller (ADF) test was applied on their first difference terms, they were stationary. The results show that all variables included are integrated of order 1, which is 1(1). After assessing the univariate time-series attributes of the individual data series, then we turned to the next stage in the current system of estimation, that is the test for co-integration (necessary condition for the specification of error correction model). The results showed that changes in maize output were jointly explained by maize farm gate price, relative humidity, one-year lagged maize output, one-year lagged maize farm gate price and one-year lagged relative humidity. Changes in rice output were jointly explained by rice farm gate price, rainfall, temperature, one-year lagged rice output and one-year lagged rice farm gate price. Therefore, if agricultural output is to be increasingly sustained, agricultural methods that are resilient to climate fluctuations are needed, as are methods to mitigate the impact of climate variability in each agricultural zone.