Background: The gubernacular canal (GC) is an important dental structure that enables the alveolar bone ridge cohesion of permanent teeth, although GC absence may indicate a dental eruption that might be associated with certain syndromes such as Down’s syndrome. This study aims to correlate the eruptive delay of permanent teeth in individuals with Down’s syndrome (Ds) and the gubernacular canal (GC) through cone-beam computed tomography (CBCT). Methods and Results: This cross-sectional study was conducted between January and July 2022 with a total of 31 individuals (G1 = 16 nonsyndromic and G2 = 15 Down’s syndrome) who went through imaging evaluation using CBCT with the following acquisition parameters: tube voltage of 95 kVp, tube current of 7 mA, exposure time of 5.9 s and voxel sizes and field of view 0.15 mm and 0.30 mm, respectively. The imaging evaluation was to assess whether all teeth analyzed had the presence of GC and/or teeth eruption disturbance, with a descriptive statistical analysis of relative frequencies and quantitative variables as well as the p-value (p < 0.005) by G Test. Results: A total of 618 teeth among 31 individuals were analyzed, 475 (76.8%) GC were detected by CBCT in 23/31 patients and of these, 6 belonged to G2. G2 had a decreased GC detection rate (n = 180–37.9%) and the most common tooth with GC detected was the mandibular 1st molar (21 GC/25 teeth—84%) and the absence of GC was most frequently observed in impacted and delayed/unerupted teeth of Ds individuals. Conclusion: We concluded that GC absence was higher among Ds individuals, explaining the increased rates of unerupted or impacted teeth in Ds individuals.