Introduction Orthodontic diagnosis and treatment planning encounter distinctive complexities when dealing with cleft lip and palate anomalies. This research endeavors to thoroughly examine skeletal and dental characteristics through cephalometric analyses among individuals with bilateral cleft lip and palate (BCLP) within the central Indian population. Due to anatomical variations and growth constraints, traditional cephalometric mean values derived from standard population studies are often inadequate for these cases. Advanced technology, such as NemoCeph (Nemotech, Madrid, Spain) software, enhances measurement accuracy. Methods Fifty patients, including 25 with BCLP and 25 without BCLP, aged 10 to 18, were selected for this cross-sectional study. Lateral cephalograms were traced and analyzed using NemoCeph software. Skeletal and dental parameters were measured, and a comparison was made between BCLP patients and the general population. Statistical analysis was conducted using the Student's unpaired t-test. Both SPSS Statistics Version 24.0 (IBM Corp., Armonk, NY, USA) and GraphPad Prism Version 7.0 (GraphPad Software, San Diego, CA, USA) were used for data analysis. Results The investigation revealed significant disparities across several parameters, including sella-nasion-A point angle (SNA), sella-nasion-B point angle (SNB), A point-nasion-B point angle (ANB), the inter-incisal angle (the angle between the long axes of the upper and lower incisors), and UP 1 to A-pog (a specific vertical measurement between anatomical markers labeled "upper 1" and "A point to pogonion"), with associated p-values for the skeletal and dental parameters of 0.310, 0.259, 0.195, 0.0001, and 0.0001, respectively. A comparison between manual tracing and digital methods indicated a reduction in errors and an improvement in measurement precision. Notably, patients diagnosed with BCLP exhibited distinctive skeletal and dental traits, highlighting the necessity for tailored treatment approaches. Conclusion This study emphasizes the importance of personalized cephalometric evaluations for patients with BCLP. Standard mean values may not be applicable due to unique anatomical considerations in these cases. Advanced technology and patient-specific assessments are crucial for accurate diagnosis, treatment planning, and orthognathic procedures in individuals with cleft lip and palate conditions. Embracing digital tools and tailored approaches can enhance patient care quality and lead to better clinical outcomes.