Hair analysis of endocannabinoids and N-acylethanolamines presents a promising methodological advancement for the retrospective assessment of long-term cumulative endocannabinoids and N-acylethanolamines secretion over extended periods of time. A main assumption of this method application that hair endocannabinoid and N-acylethanolamine concentrations show intra-individual stability has not been confirmed yet. Thus, in the current study hair endocannabinoid and N-acylethanolamine levels were measured over a period of two and a half years with six months between each hair sample collection in 100 female participants. We found strong test-retest associations of hair endocannabinoid and N-acylethanolamine levels with intraclass correlation coefficients between 0.79 and 0.92. Furthermore, no correlations between perceived stress and hair endocannabinoids or N-acylethanolamines was observed. The current findings support the notion that endocannabinoids and N-acylethanolamines in hair are rather trait biomarkers that are stable over a considerable period of time rather than rapidly changing state markers.