Abstract Observations of the merger of Jupiter's White Ovals BE and FA show altitude-dependent behavior that we seek to capture in numerical simulations. In particular, it was observed that the upper portions of the vortices orbited each other before merging, but the lower portions translated into each other without orbiting, a phenomenon we term the pair-orbit vertical dichotomy. To reproduce this dichotomy in the EPIC model, it is sufficient to have (i) a decrease with altitude of the background zonal winds above the cloud level with a scale height of ∼2.4, (ii) a height scale of the winds inside the vortices that is the same or larger, and (iii) a maximum tangential velocity in each vortex of ∼100 m s−1 or larger. Condition (i) is expected from thermal-wind analyses, (ii) is consistent with thermal-wind and Shoemaker–Levy 9 debris-trajectory analyses, and (iii) is consistent with cloud-top wind tracking. The model generally does not reproduce the dichotomy for vortices with smaller vertical extent or weaker circulations. Our simulated mergers correctly reproduce the observed ∼9° separation at which vortices start to orbit in the upper layers before they merge and the ∼70% area ratio of the final vortex BA to the sum of BE and FA.