This study aimed to compare the annualized segmental cervical spinal cord atrophy rate (ASCAR) in the early and late stages of relapsing remitting multiple sclerosis (RRMS), and to investigate the relationship between ASCAR and no evidence of disease activity (NEDA) in RRMS. Participants in this study included early stage MS (EMSg) patients, late stage MS (LMSg) patients, and healthy controls. All of the included participants (n = 175 subjects) were followed up for 14 months, and an MRI was performed on each participant at the beginning and at the end of the study. Cervical spinal cord average segmental area (CSCA) was measured by a semi-automated method, and ASCAR (mm(2)/year) was calculated. Data from the EMSg (n = 81 subjects) and LMSg (n = 94 subjects) patient groups were compared with each other and with the control group (n = 43 subjects). Examination of the initial CSCA values revealed that the baseline CSCA of the control group was larger than that of the EMSg (p < 0.001), and the baseline CSCA of the EMSg was larger than that of the LMSg (p < 0.001). The ASCAR of the control group, LMSg, and EMSg were 0.48, 0.93, and 1.81 mm(2) (p < 0.001), respectively. Regression analysis revealed that disability increase was associated with ASCAR, while MRI activity and relapse presence were unrelated to ASCAR. In both patient groups, ASCAR was slower in those who fulfilled NEDA but this relationship was not significant. Cervical spinal cord atrophy progression over time occurs at a greater rate in the early stages of RRMS disease compared to the late stages. ASCAR was unrelated to MRI activity and relapse, which are clinical markers of acute inflammation.