The utility of urine and serum hepcidin measurements in the clinic depends on their reproducibility. We sought to expand our previous work on the within-subject variability and between-subject variability of this novel iron parameter in the serum and urine of 24 healthy controls by time-of-flight mass spectrometry at four different time points during the day. A linear mixed model for repeated data was used to distinguish three components of the total variability in the measurements: within-day/within-subject variability, between-subject variability, and additional residual or (pre)analytical variability. Differences in diurnal hepcidin patterns were observed between urine and serum. Urine levels remained similar during the course of the morning and increased significantly during the afternoon, whereas serum levels increased significantly throughout both the morning and afternoon. Furthermore, in serum the (pre)analytical variability (28.6%) was smaller than the between-subject (48.1%) and within-day/within-subject variability (30.3%) compared with urine variability (97.2% vs. 67.7 and 77.3%, respectively). High serum ferritin levels were associated with higher serum hepcidin levels but not with urine levels. Transferrin saturation did not correlate with hepcidin levels. To minimize variability, we recommend (i) standardizing for sampling time and (ii) measuring serum hepcidin levels.