Uncertainty assessment techniques have been extensively applied as an estimate of accuracy to compensate for weaknesses with traditional approaches. Traditional approaches to mapping accuracy assessment have been based on a confusion matrix, and hence are not only dependent on the availability of test data but also incapable of capturing the spatial variation in classification error. Here, we apply and compare two uncertainty assessment techniques that do not rely on test data availability and enable the spatial characterisation of classification accuracy before the validation phase, promoting the assessment of error propagation within the classified imagery products. We compared the performance of emerging deep neural network (DNN) with the popular random forest (RF) technique. Uncertainty assessment was implemented by calculating the Shannon entropy of class probabilities predicted by DNN and RF for every pixel. The classification uncertainties of DNN and RF were quantified for two different hyperspectral image datasets—Salinas and Indian Pines. We then compared the uncertainty against the classification accuracy of the techniques represented by a modified root mean square error (RMSE). The results indicate that considering modified RMSE values for various sample sizes of both datasets, the derived entropy based on the DNN algorithm is a better estimate of classification accuracy and hence provides a superior uncertainty estimate at the pixel level.