The objective of this study was to investigate the profiles of hair cortisol concentrations as an index of chronic stress in dairy cows in association with their health, nutrition, and reproductive parameters. For 25 Holstein dairy cows, hair was collected from the tail switch −19.2 ± 11.4, 44.8 ± 11.9, 103.0 ± 9.9, and 168.0 ± 9.7 days postpartum (L0, L1, L2, and L3, respectively). Body condition scores were negatively correlated with hair cortisol concentrations (r = −0.255), and hock health scores were positively correlated with hair cortisol concentrations (r = 0.236, p < 0.05). Hair cortisol concentrations during the postpartum period showed different patterns according to the time of first artificial insemination (AI) and fertility. Cows that were submitted to first AI by 86 days postpartum showed a peak hair cortisol concentration at L1, whereas cows with delayed first AI had a peak at L2. The hair cortisol concentrations of subfertile (≥168 days) cows were significantly higher at L1 and L2 compared with L0, whereas hair cortisol concentrations of fertile cows (<168 days) were not different among the sampling times. These results indicate that cows with health problems appear to experience greater chronic stress, which may impair their reproductive function.