The endocannabinoid system is considered to play a role in a wide range of functions, including stress. Hair analysis of endocannabinoids presents a promising methodological advancement for the retrospective assessment of long-term cumulative endocannabinoid secretion. Despite promising pilot study results suggesting the usefulness of hair endocannabinoid assessments, it remains unclear whether hair endocannabinoid levels mirror systemic endocannabinoid levels accurately. Two independent studies were conducted to investigate to what extent hair endocannabinoid and N-Acylethanolamine levels reflect the systemic levels retrospectively. Endocannabinoid and N-Acylethanolamine levels were measured in 3 cm and 1 cm hair segments respectively, and compared with the averaged levels in multiple plasma samples collected during three months (Study I), and in multiple 24-hour urine samples collected over a month (Study II). In addition, the Perceived Stress Scale was used to assess the perceived stress throughout the studies. Against our hypothesis, no association was found between the endocannabinoid or N-Acylethanolamine levels in hair and plasma or urine. However, hair palmitoylethanolamide (PEA), oleoylethanolamide (OEA), and stearoylethanolamide (SEA) levels were positively correlated with perceived stress in Study I. The current findings suggest that hair endocannabinoid or N-Acylethanolamine levels might not accurately reflect the levels of peripheral circulating endocannabinoid or N-Acylethanolamine. Nevertheless, hair N-Acylethanolamine levels might emerge as a useful strategy in the study of some psychological phenotypes, such as stress.