Safety Performance Functions (SPFs) are regression models used to predict the expected number of collisions as a function of various traffic and geometric characteristics. One of the integral components in developing SPFs is the availability of accurate exposure factors, that is, annual average daily traffic (AADT). However, AADTs are not often available for minor roads at rural intersections. This study aims to develop a robust AADT estimation model using a deep neural network. A total of 1,350 rural four-legged, stop-controlled intersections from the Province of Alberta, Canada, were used to train the neural network. The results of the deep neural network model were compared with the traditional estimation method, which uses linear regression. The results indicated that the deep neural network model improved the estimation of minor roads’ AADT by 35% when compared with the traditional method. Furthermore, SPFs developed using linear regression resulted in models with statistically insignificant AADTs on minor roads. Conversely, the SPF developed using the neural network provided a better fit to the data with both AADTs on minor and major roads being statistically significant variables. The findings indicated that the proposed model could enhance the predictive power of the SPF and therefore improve the decision-making process since SPFs are used in all parts of the safety management process.