Background: Dermatoglyphics, the study of unique, immutable epidermal ridge patterns, emerges from the same embryological ectoderm as the nervous system during early gestation. This shared origin posits it as a potential phenotypic marker for neurodevelopmental anomalies like autism spectrum disorder (ASD). Most studies are from Western populations, with a paucity of gender-stratified data from South Asia. Objectives: This study aimed to conduct a gender-wise comparative analysis of digital dermatoglyphic patterns between autistic and neurotypical children in Northern Bangladesh, to identify potential pattern deviations associated with ASD. Methods: This cross-sectional analytical study enrolled 100 Bangladeshi children aged 5–15 years: 50 diagnosed with ASD (38 male, 12 female) and 50 age-matched neurotypical controls (26 male, 24 female). Bilateral fingerprints were acquired using a ZKT ECO biometric scanner and classified into Arch (A), Ulnar Loop (UL), Radial Loop (RL), and Whorl (W) patterns using DigiDoctors software (v1.0.1). Statistical analysis was performed using SPSS v23.0, employing Chi-square and Fisher’s exact tests where appropriate. A p-value <0.05 was considered significant. Results: Significant inter-group differences were observed (p<0.001). The autistic group exhibited a higher frequency of: Arch (12.6% vs. 4.4%; OR=3.15, 95% CI: 1.89-5.25), Whorl (36.4% vs. 32.4%), and Radial Loop (3.6% vs. 1.2%). Ulnar Loops were significantly lower in the autistic group (47.4% vs. 61.6%). Gender-stratified analysis revealed autistic males had significantly higher frequencies of Arch, Whorl, and Radial Loop compared to neurotypical males. Autistic females showed a pronounced increase in Arch pattern (16.67% vs. 2.92%; p<0.001) but lower frequencies of Whorl and Radial Loop. Radial Loops were absent in autistic females. Conclusion: This study provides the first gender-stratified dermatoglyphic profile of autistic children in Bangladesh, revealing distinct pattern deviations that differ between males and females. The findings support the hypothesis of altered ectodermal development in ASD and suggest dermatoglyphics could serve as a low-cost, non-invasive adjunctive tool in multidisciplinary ASD assessment, particularly in resource-limited settings. Further large-scale, familial, and genetic correlational studies are warranted.