Introduction Multiple sclerosis (MS) is a chronic and autoimmune disease that has a significant influence on the central nervous system, such as the brain and spinal cord, affecting millions of individuals globally. Understanding the connection between subcortical brain regions and MS is crucial for effective diagnostic and therapeutic approaches for treating this disabling disease. This study explores the relationship between volume and contours of asymmetry index of subcortical brain regions in individuals with MS using volBrain software (https://www.volbrain.net; developed by José V.Manjón (Valencia Polytechnic University, Valencia, Spain) and Pierrick Coupé (University of Bordeaux, Bordeaux, France)). Methods In our retrospective investigation, we admitted 100 Turkish individuals, comprising 50 patients diagnosed with relapsing-remitting MS (RRMS) (24 (48%) males and 26 (52%) females) and 50 healthy controls (23 (46%) males and 27 (54%) females), registered between October 2017 and February 2022 for five years and underwent assessment in the radiology department at the Teaching and Research Hospital of Kocaeli University; 1,150 Turkish patients were excluded from our study based on our exclusion criteria. We used magnetic resonance imaging with a 3-Tesla (3T) scanner and volBrain software to assess volumes (cm3) and asymmetry indexes due to asymmetry for different levels of atrophy of total intracranial, total brain, gray matter, white matter, and subcortical regions, the most affected regions in MS patients for both patient and control cohorts. Results Statistical analysis revealed a significant difference between patient and control groups (p < 0.001), with patient group mean age at 38.32 years and control group mean age at 32.88 years. Patient group exhibited lower values for total intracranial, total brain, gray matter, white matter, and cerebrospinal fluid volume compared to control group (p < 0.05). The results indicated a statistically significant decrease (p < 0.05) in the values for total intracranial and total brain volume, whereas all other values remained unchanged. We compared volumes of subcortical structures on the right and left sides and found that the putamen, thalamus, and globus pallidus had statistically lower values in the patient group than in the control group (p < 0.001), apart from the lateral ventricle. Furthermore, our retrospective investigation demonstrated a statistically significant difference in the globus pallidus asymmetry index, indicating a preference for the patient group (p < 0.05). A lower asymmetry index value signifies a larger volume for the right side of the subcortical regions of the brain when compared to the left side. Conclusion Brain atrophy, although characterized by irreversible tissue damage, is targeted by therapeutic interventions to prevent progression. It is, therefore, imperative to develop a universally accepted measurement standard for subcortical structures that also considers the inherent variability present within each structure. Our findings serve as an important basis and indicator for the determination of subcortical atrophy and asymmetry in MS, the prognosis of the disease, and the etiology of clinical symptoms. Subsequent research may benefit by adopting the novel approach of considering brain atrophy as an outcome rather than a predictor, thereby facilitating the elucidation of the intricate biological mechanisms that give rise to volume loss.