Purpose The aim was to quantify inter- and intra-observer variability in manually delineated hepatocellular carcinoma (HCC) lesion contours and the resulting impact on radioembolization (RE) dosimetry. Methods Ten patients with HCC lesions treated with Y-90 RE and imaged with post-therapy Y-90 PET/CT were selected for retrospective analysis. Three radiologists contoured 20 lesions manually on baseline multiphase contrast-enhanced MRIs, and two of the radiologists re-contoured at two additional sessions. Contours were transferred to co-registered PET/CT-based Y-90 dose maps. Volume-dependent recovery coefficients were applied for partial volume correction (PVC) when reporting mean absorbed dose. To understand how uncertainty varies with tumor size, we fit power models regressing relative uncertainty in volume and in mean absorbed dose on contour volume. Finally, we determined effects of segmentation uncertainty on tumor control probability (TCP), as calculated using logistic models developed in a previous RE study. Results The average lesion volume ranged from 1.8 to 194.5 mL, and the mean absorbed dose ranged from 23.4 to 1629.0 Gy. The mean inter-observer Dice coefficient for lesion contours was significantly less than the mean intra-observer Dice coefficient (0.79 vs. 0.85, p < 0.001). Uncertainty in segmented volume, as measured by the Coefficient of Variation (CV), ranged from 4.2 to 34.7% with an average of 17.2%. The CV in mean absorbed dose had an average value of 5.4% (range 1.2–13.1%) without PVC while it was 15.1% (range 1.5–55.2%) with PVC. Using the fitted models for uncertainty as a function of volume on our prior data, the mean change in TCP due to segmentation uncertainty alone was estimated as 16.2% (maximum 48.5%). Conclusions Though we find relatively high inter- and intra-observer reliability overall, uncertainty in tumor contouring propagates into non-negligible uncertainty in dose metrics and outcome prediction for individual cases that should be considered in dosimetry-guided treatment.