Autophagy is a catabolic process for the removal of damaged organelles and energy retrieval in which cytoplasmic material and damaged organelles are engulfed in double membrane vesicles and delivered to the lysosomes for degradation. This process is critical for cellular and tissue homeostasis. Previous studies indicated that in dividing cells mTORC1 activity inhibits autophagy, thus TSC1/2-loss results in reduced autophagic organelles. Despite the involvement of the mTORC1 pathway in autophagy and its critical role in neuronal function, most of the knowledge on the effect of mTORC1 activity on autophagy was based on studies performed using dividing cells. Here, we demonstrate that, unlike in fibroblasts, loss of TSC1/2 function by Tsc2 gene knockdown in rat hippocampal neurons results in autophagy initiating signals. Our data also indicate that TSC-deficient neurons display accumulation of autolysosomes and autophagy initiation via the activation of AMPK-dependent regulation of ULK1. In addition to our observations in cultured neurons, in vivo data from Tsc1 mouse models and from cortical tissue resected from TSC patients at the time of epilepsy surgery support our finding that neuronal loss of TSC1/2 initiates a paradoxical AMPK-dependent increase in autophagic flux. These findings have important implications for TSC disease, where aberrant autophagic flux likely contributes to the metabolic and synaptic abnormalities in the brain leading to neurological symptoms such as epilepsy, intellectual disability and autism. They also provide new insights about the role of mTORC1 and autophagy in other neurological conditions with accumulation of toxic aggregates such as Alzheimer’s and Parkinson’s diseases.