A reputation for coarse root systems with dominant taproots, and for slow shoot development among seedlings, limits use of hickory species (Carya Nutt.) that could increase diversity in managed landscapes. We examined effects of root pruning and application of auxin on root and shoot development of seedlings of several species of hickory. Our hypothesis was that pruning the radicle shortly after seed germination and subsequent treatment with auxin would increase root branching without curtailing development of the shoot. Germinated seeds of Carya aquatica (F. Michx.) Nutt., Carya cordiformis (Wangenh.) K. Koch, Carya laciniosa (F. Michx.) Loudon, Carya ovata (Mill.) K. Koch, and Carya tomentosa (Lam.) Nutt. were treated by removing two-thirds of the length of the radicle with and without immediate application of 3000 mg·L−1 indole-3-butyric acid (IBA) via Hormex rooting powder #3 to the remaining one-third of radicle. Neither treatment altered stem height, stem caliper, or root dry weight. After 75 days, root-pruned seedlings of Carya ovata without auxin had 42% fewer fibrous first-order lateral roots than did unpruned controls. Root pruning plus auxin led to a 79% increase in the number of fibrous first-order lateral roots of C. laciniosa and an ≈50% increase in the shoot dry weight of C. aquatica. Both root pruning and root pruning plus auxin evoked formation of taproot branches for all species. Because species differed in responses of root and shoot systems to root pruning with and without auxin, the practice should be implemented cautiously based on the species.