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Background: Orthodontic appliances can interfere with routine oral hygiene and promote plaque retention, leading to gingival inflammation during active treatment. While self-ligating fixed appliances were introduced to reduce plaque accumulation compared with conventional braces, clear aligner therapy has gained popularity due to its removable design and perceived periodontal advantages. Evidence directly comparing the periodontal impact of these two appliance systems under randomized clinical conditions remains limited. Objective: To compare changes in plaque accumulation and gingival inflammation in patients undergoing orthodontic treatment with clear aligners versus self-ligating fixed appliances during the early phase of active treatment. Methods: A parallel-arm randomized controlled trial was conducted over four months in the Islamabad–Rawalpindi region. Sixty orthodontic patients aged 18–30 years were randomly allocated to receive either clear aligners or self-ligating braces. Periodontal status was assessed at baseline, two months, and four months using the Silness and Löe Plaque Index and the Löe and Silness Gingival Index. Data were analyzed using independent t-tests, repeated measures ANOVA, and Pearson correlation analysis, with statistical significance set at p < 0.05. Results: Fifty-eight participants completed the study. Both groups showed increases in plaque and gingival index scores over time; however, these increases were significantly greater in the self-ligating brace group. At four months, mean plaque index scores were 1.02 ± 0.26 in the clear aligner group and 1.38 ± 0.31 in the self-ligating group (p < 0.001). Mean gingival index scores were 0.94 ± 0.23 and 1.31 ± 0.28, respectively (p < 0.001). A strong positive correlation was observed between plaque accumulation and gingival inflammation (r = 0.68, p < 0.001). Conclusion: Clear aligner therapy was associated with more favorable periodontal outcomes than self-ligating fixed appliances during early orthodontic treatment. Appliance removability appeared to support better plaque control, underscoring the importance of appliance selection and oral hygiene reinforcement in orthodontic care.