We hypothesized that postoperative sedation with dexmedetomidine/fentanyl would be effective in infants and neonates with congenital heart disease and pulmonary arterial hypertension (PAH). Children who were <36 months of age, had congenital heart disease with PAH, and had been treated at our hospital between October 2011 and April 2013 (n = 187) were included in this retrospective study. Either dexmedetomidine/fentanyl (Group Dex) or midazolam/fentanyl (Group Mid) was used for postoperative sedation. The main outcome variables included delirium scores, supplemental sedative/analgesic drugs, ventilator use, and sedation time. Baseline demographics and clinical characteristics were similar between the two groups. The Pediatric Anesthesia Emergence Delirium scale (5.2 ± 5.3 vs. 7.1 ± 5.2 in the Dex and Mid groups, respectively; P = 0.016) and the incidence of delirium (18.2 vs. 32.0 % in the Dex and Mid groups, respectively; P = 0.039) were significantly lower in the Dex group than in the Mid group. Total sufentanil, midazolam, and propofol doses given during the operation did not differ between the two groups. Group Dex patients required significantly lower doses of adjunctive sedative/analgesic drugs than group Mid patients in the cardiac intensive care unit (CICU; midazolam, P = 0.007; morphine, P < 0.001). In conclusion, we found no differences between dexmedetomidine/fentanyl and midazolam/fentanyl in terms of the duration of sedation, mechanical ventilator use, and CICU stay in children with PAH. However, patients in the Dex group required a lower additional sedative/analgesic drugs and had a lower incidence of delirium than patients in the Mid group.