In many real-world applications, e.g., monitoring of individual health, climate, brain activity, environmental exposures, among others, the data of interest change smoothly over a continuum, e.g., time, yielding multidimensional functional data. Solving clustering, classification, and regression problems with functional data calls for effective methods for learning compact representations of functional data. Existing methods for representation learning from functional data, e.g., functional principal component analysis, are generally limited to learning linear mappings from the data space to the representation space. However, in many applications, such linear methods do not suffice. Hence, we study the novel problem of learning non-linear representations of functional data. Specifically, we propose functional autoencoders, which generalize neural network autoencoders so as to learn non-linear representations of functional data. We derive from first principles, a functional gradient based algorithm for training functional autoencoders. We present results of experiments which demonstrate that the functional autoencoders outperform the state-of-the-art baseline methods.