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Background Mitral stenosis (MS) is a common valvular heart disease that is frequently complicated by arrhythmias, heart failure, pulmonary hypertension, and thromboembolic events. This study aimed to determine the clinical and echocardiographic factors of complications in patients with MS. Methodology This retrospective cross-sectional study was conducted at the Cardiology Department of Northwest General Hospital and Research Centre, Peshawar, including 121 patients diagnosed with MS using echocardiography. Patients of either gender, aged ≥18 years, and diagnosed with MS confirmed by transthoracic echocardiography (either rheumatic or non-rheumatic) with complete clinical and echocardiographic data were included in the study. Complications were assessed at the time of initial hospital evaluation and defined as the presence of one or more disease-related adverse conditions attributable to MS, including atrial fibrillation or other clinically significant arrhythmias, heart failure, pulmonary hypertension, thromboembolic events (ischemic stroke or systemic embolism), left atrial thrombus, and respiratory complications secondary to pulmonary congestion or hypertension. Information regarding demographics, pre-existing comorbid conditions, New York Heart Association (NYHA) functional class, and multiple echocardiographic parameters was recorded. Data were analyzed using SPSS Statistics version 27 (IBM Corp., Armonk, NY, USA). Associations were assessed using chi-square and independent t-tests. Multivariate logistic regression identified independent factors. A p <0.05 was considered significant. Results The mean age was 57.4±16.8 years, with female predominance (63.6%). Diabetes mellitus and hypertension were present in 34.3% and 27.8% patients, respectively. Overall, 38 patients (31.4%) developed complications; arrhythmias (10.7%) and heart failure (9.3%) were most frequent, while stroke occurred in 1.7%. On univariate analysis, female sex (odds ratio (OR) 1.91, p=0.048), diabetes mellitus (OR 2.31, p=0.032), hypertension (OR 2.11, p=0.041), NYHA class III-IV (OR 3.18, p=0.003), severe MS (OR 5.38, p<0.001), pulmonary artery systolic pressure (PASP) >50 mmHg (OR 3.57, p=0.002), and left atrial diameter ≥50 mm (OR 3.44, p = 0.001) were significantly associated with complications. Multivariate analysis identified severe MS (adjusted OR (AOR) 3.58, CI 1.62-7.89, p=0.002), PASP >50 mmHg (AOR 3.12, CI 1.41-6.91, p=0.005), left atrial diameter ≥50 mm (AOR 2.74, CI 1.21-6.20, p=0.016), diabetes mellitus (AOR 2.29, CI 1.03-5.10, p=0.041), and NYHA class III-IV (AOR 2.88, CI 1.29-6.45, p=0.010) as independent factors. Conclusion Complications in MS are driven by both clinical and echocardiographic factors. Integrated assessment may improve risk stratification and guide timely management.