In Parkinson's disease (PD), neuronal loss occurs in the substantia nigra (SN) and locus coeruleus (LC). Previous studies using neuromelanin-sensitive magnetic resonance imaging (NMI) at 3T MRI have described the measurement methods and diagnostic significance of the contrast ratio (SN-CR) and area (SN-A), as well as their association with clinical symptoms. However, no reports have evaluated the consistency of NMIs acquired using different MR protocols in the same patients over a short period. Therefore, this study evaluated the similarity of two-dimensional (2D) NMIs obtained simultaneously under different imaging parameters. The SN-CR, LC-CR, and SN-A were compared in 54 of 55 patients with PD who underwent 2D NMIs within 3 months under different imaging conditions, with one patient excluded due to artifacts. The relationships of these variables with motor and cognitive function were then examined. The mean age of the cohort was 62.3 ± 8.0 years. The mean disease duration was 11.4 ± 5.2 years, and the male-to-female ratio was 25:29. No significant correlation was found for SN-CR (r = 0.233, p = 0.091) and LC-CR (ρ = 0.180, p = 0.192). However, a significant, albeit weak, positive correlation was observed for SN-A (ρ = 0.403, p = 0.003). Standardization of imaging protocols is essential to minimize technical variability.