Background and Objectives: More frequent and severe droughts are occurring due to climate change in northern China. In addition to intensity and duration, the timing of droughts may be decisive for its impacts on tree growth, mortality, and the whole forest ecosystem. The aim of this study was to compare the effect of drought occurring in the early- and mid-growing season on the growth and physiology of Mongolian pine (Pinus sylvestris var. mongolica Litv.) saplings. Materials and Methods: Four-year-old container saplings that were about to sprout were exposed to three treatments: (i) regular irrigation throughout the growing season (CTRL), (ii) no irrigation in the early growing season (weeks 1–5) followed by regular irrigation (EGD), (iii) no irrigation in the mid growing season (weeks 5–10), and regular irrigation in the early and late growing season (MGD). We measured the root and shoot growth, sapling mortality, and the physiological changes in the roots and needles periodically. Results: Drought in the mid growing season was more harmful than in the early growing season in terms of chlorophyll fluorescence, electrolyte leakage of needles, needle length, stem diameter increment, and sapling mortality. The high mortality in the mid growing season might be attributed to the joint effect of drought and high temperature. Drought in the early growing season decreased root growth, and the starch and soluble sugars in roots as much as the drought in the mid growing season. Abscisic acid concentration increased in fine roots, but decreased in old needles after drought. Conclusions: Special attention should be paid on forest sites susceptible to drought during afforestation in the face of ongoing climate change.