Background: This study evaluate the comfort of two widely used intraoral scanning devices, Itero™ and 3Shape™, in pediatric patients. Methods: A total of 68 children aged 9–12 years in the mixed dentition period participated in this single-center, analytical, controlled cross-sectional study. Comfort levels were assessed using the Animated Emoji Scale (AES) following intraoral scanning. Statistical analyses were conducted with a 95% confidence level (p ≤ 0.05). Results: No statistically significant difference was observed between the two devices in terms of gender-based comfort (p > 0.05), and the participants did not report pain, nausea, or breathing difficulties with either device (p > 0.05). The performance times of both scanners were comparable (p > 0.05). Although no dry mouth sensation was reported, children exhibited greater engagement with the screen when using the Itero™ scanner (p > 0.05). The 3Shape™ scanner was significantly louder than the Itero™ (p < 0.05), while the intraoral camera head of the Itero™ was perceived as less comfortable than that of the 3Shape™ (p < 0.05). Conclusions: Pediatric patients were generally satisfied with both intraoral scanning procedures, and factors such as a smaller intraoral camera head, quieter operation and larger display screens were identified as important for enhancing patient comfort.