Background: Transarterial radioembolization (TARE) relies on directly injected 90Y- or 166Ho-loaded microspheres in the hepatic arteries. The activity to be injected is generally based on pre-TARE 99mTc-macro-aggregated-albumin (MAA) imaging, while the actual dose distribution is based on post-treatment images. The volume of interest (VOIs) propagation methods (i.e., rigid and deformable) from pre- to post-TARE imaging might affect the estimation of the mean absorbed dose in the tumor and non-tumoral liver (NTL), i.e., DT and DNTL, respectively. Methods: In 101 consecutive patients, liver and tumor were delineated on pre-TARE images and semi-automatically transferred on 90Y-PET/CT images with a rigid or deformable registration approach. Pre- and post-TARE volumes and DT/DNTL/DL were compared using correlation coefficient (CC) indexes, such as intra-class (ICC), Pearson’s (PCC), concordance (CCCo) and Bland–Altman analyses. The Kaplan–Meier curves of overall survival (OS) were calculated according to DT. Results: All computed CCs indicated very good (>0.92) agreement for volume comparison, while they suggested good (ICC ≥ 0.869, PCC ≥ 0.876 and CCCo ≥ 0.790) and moderate agreement in the intra- and inter-modality DT/DNTL/DL comparisons, respectively. Bland–Altman analyses showed percentage differences between the manual and deformable approaches of up to about −31%, 9% and 62% for tumoral volumes, DT and DNTL, respectively. The overall survival analysis showed statistically significant differences using DT cutoffs of 110, 90 and 85 Gy for the manual, rigid and deformable approaches, respectively. Conclusions: The semi-automatic transfer of VOIs from pre- and post-TARE imaging is feasible, but the selected method might affect prognostic DT/DNTL constraints.