Abstract Background Goniometry can be performed clinically in dogs with cranial cruciate ligament disease (CCLD). The purpose of this study was (1) to compare reliability of stifle goniometry in dogs with CCLD and healthy dogs and (2) to investigate the effect of compliance on measurements. Dogs presented for surgical intervention for CCLD (CCL-Dogs; n = 15) and orthopedically healthy dogs (C-Dogs; n = 11) were enrolled in this prospective randomized controlled trial. In each dog, three observers randomly measured maximum stifle flexion (mSF) and maximum stifle extension (mSE) three times with a standard goniometer with the scale covered, while dog compliance was scored (Scores: C0: excellent - C4: poor). Intraclass correlation coefficient (ICC) was calculated for intra-/interobserver reliability. Effects on measurements were evaluated with mixed-effect models (MEM). Results Maximum stifle extension and mSE-compliance were significantly decreased in CCL-Dogs compared to C-Dogs (p ≤ 0.004), but mSF and mSF-compliance did not differ between groups. Intraobserver reliability was excellent for all dogs during mSE (ICC:0.75–0.99) and mSF (ICC:0.89–0.99). Interobserver reliability was excellent for mSF in both groups (ICC: C-Dogs:0.84, CCL-Dogs:0.9) and for mSE in CCL-Dogs (ICC:0.94) but only fair for mSE in C-Dogs (ICC:0.58). Robust MEM showed that the combined average of all mSE measurements of all three observers was affected by compliance in both groups (p < 0.001). This effect was not observed for single mSE-measurements by themselves. Conclusion The results of this study indicate that compliance may affect goniometric stifle extension measurements in healthy and CCLD dogs. In a clinical setting, intra-/interobserver reliability was excellent for all measurements except for maximum stifle extension in healthy dogs.