Circadian rhythm abnormalities, including sleep-wake disturbances, are common features of neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Although pathological aggregation and cytoplasmic mislocalization of TDP-43 is a key event in ALS/FTD, the relationship between this protein and circadian rhythms remains unclear. We developed new Drosophila TDP-43 models to investigate its role in rhythmicity, sleep and memory. In young male adult flies, overexpression of wild type hTDP-43 (WT) in circadian neurons showed no impact on rhythmicity. The period (Tau) was not different from control animals, with a trend for decreased Tau power. In contrast, sleep analysis revealed increased sleep bouts and mean sleep length during night, but decreased total sleep duration during day. Conversely, overexpression of a hTDP-43 variant with a mutated nuclear localization signal (ΔNLS) led to a complete disruption of circadian rhythms, with no flies showing identifiable period. Surprisingly, sleep was not disturbed. When analyzing the effect of hTDP-43 overexpression in mushroom bodies neurons over inhibitory control of proboscis extension reflex, both WT and ΔNLS young flies showed memory indexes indistinguishable from control group. These results define cytoplasmic TDP-43 mislocalization as a key player in circadian disturbances, and provide new evidence for the role of this protein in human diseases of the ALS/FTD spectrum.