Circadian rhythms and their involvement with various human diseases, including neurological disorders, have become an intense area of research for the development of new pharmacological treatments. The location of the circadian clock machinery in the central nervous system makes it challenging to reach molecular targets at therapeutic concentrations. In addition, a timely administration of the therapeutic agents is necessary to efficiently modulate the circadian clock. Thus, the use of nanoparticles in circadian clock dysfunctions may accelerate their clinical translation by addressing these two key challenges: enhancing brain penetration and/or enabling their formulation in chronodelivery systems. This review describes the implications of the circadian clock in neurological pathologies, reviews potential molecular targets and their modulators and suggests how the use of nanoparticle-based formulations could improve their clinical success. Finally, the potential integration of nanoparticles into chronopharmaceutical drug delivery systems will be described.