Aim: To investigate the root canal morphology of hypomineralised first permanent molars (FPMs) using micro-CT (μCT). Methodology: Twenty-four hypomineralised FPMs and five clinically sound FPMs were scanned using μCT and assessed using the following parameters: (i) root canal configuration, (ii) connecting canal frequency, (iii) enamel, dentin, and pulp volumes, (iv) cusp tip to pulp horn distance, root canal length, root canal width, and dentin thickness, and (v) the influence of the root canal system landmarks on access cavity outline forms and canal curvature. A two-way repeated-measures analysis of variance was employed with the statistical significance set at p < 0.05. Results: The frequency of accessory and connecting canals was higher in hypomineralised FPMs. Mesio-buccal cusp horn was found to be the closest to its corresponding cusp tip in both groups. There was no significant difference between the root lengths, dentine widths, and pulp space measurements of hypomineralised FPMs compared to clinically sound FPMs. The best angulation to access FPMs was straight-line radicular, along the pulp horn. Conclusions: This study illustrates some variations in the root canal morphology in hypomineralised FPMs compared to clinically sound FPMs. Future studies should focus on assessing these parameters in larger samples.