<b><i>Purpose:</i></b> We examined select pulmonary effects and donor cell kinetics after transamniotic stem cell therapy (TRASCET) in a model of congenital diaphragmatic hernia (CDH). <b><i>Methods:</i></b> Pregnant dams (<i>n</i> = 58) received nitrofen on gestational day 9.5 (E9) to induce fetal CDH. Fetuses (<i>n</i> = 681) were divided into 4 groups: untreated (<i>n</i> = 99) and 3 groups receiving volume-matched intra-amniotic injections on E17 of either saline (<i>n</i> = 142), luciferase-labeled amniotic fluid-derived mesenchymal stem cells (afMSCs; <i>n</i> = 299), or acellular recombinant luciferase (<i>n</i> = 141). Pulmonary morphometry, quantitative gene expression of pulmonary vascular tone mediators, or screening for labeled afMSCs were performed at term (E22). Statistical comparisons were by Mann-Whitney U-test, nested ANOVA, and Wald test. <b><i>Results:</i></b> TRASCET led to significant downregulation of endothelial nitric oxide synthase and endothelin receptor-A expressions compared to both untreated and saline groups (both <i>p</i> < 0.001). TRASCET also led to a significant decrease in arteriole wall thickness compared to the untreated group (<i>p</i> < 0.001) but not the saline group (<i>p</i> = 0.180). Donor afMSCs were identified in the bone marrow and umbilical cord (<i>p</i> = 0.035 and 0.015, respectively, vs. plain luciferase controls). <b><i>Conclusions:</i></b> The effects of TRASCET in experimental CDH appear to be centered on the pulmonary vasculature and to derive from circulating donor cells.