Commercial banks play a crucial role in the agricultural sector in advancing affordable credit to improve their productivity, enhancing their food security, and expanding their income. Financing of the sector however continues to get the lowest levels of credit in Kenya compared to other sectors due to poor loan repayment. The objectives of the study were to establish the effect of Gross Domestic Product, determine the effect of real effective exchange rate; determine the effect of lending rate on agricultural non-performing loans, and to assess the effect of growth in loan portfolio on agricultural Non-performing Loan. Secondary data relating to commercial banks’ lending to the agricultural sector for a period of 7 years from 2011 to 2017 were collected and using Statistical Package for Social Science computer software to carry out regression analysis procedure, correlation, and descriptive statistics. The portfolio at risk was used as a proxy to Non-preforming agricultural Loans and calculated by dividing the amounts in default by the outstanding loans. Results showed a general increase in the real Gross Domestic Product, gross agricultural loans, and real effective exchange rate over the study period and a decrease in the loan portfolio and the lending rates. Agricultural Non-Performing Loans had a strong positive correlation with real Gross Domestic Product (0.836, p