We measured pulmonary gas exchange during six minute walk test (6MWT) in patients with idiopathic (IPAH) and congenital heart disease-related pulmonary hypertension (CHDPH), and determined the relationship between the degree of desaturation and changes in minute ventilation to carbon dioxide production and end-tidal partial pressure for carbon dioxide (PetCO2) in both groups. Fifty-two patients (IPAH, n = 28; CHDPH, n = 24) completed 6MWT with simultaneous pulmonary gas exchange. Whilst no significant difference in six minute walk distance was observed between groups (IPAH: 529 ± 89; CHDPH: 476 ± 119 m, p = 0.10), oxygen uptake, carbon dioxide production, and minute ventilation were higher in IPAH than CHDPH (p < 0.01). In addition, CHDPH desaturated to a greater extent than IPAH with a lower post-6MWT SPO2 (IPAH: 92.3 ± 7.9; CHDPH: 73.3 ± 14.9%, p < 0.01). The change in SpO2 correlated to the change in (r=−0.44, p = 0.02) and PetCO2 (r = 0.49, p < 0.01) for CHDPH, but not IPAH. The exercise-induced hypoxic stimulus during 6MWT in CHDPH may be associated with an enhanced ventilatory response.