Previous reports have identified risk factors associated with development of post-Fontan protein-losing enteropathy. Less is known about the economic impact and resource utilisation required for post-Fontan protein-losing enteropathy in the current era. We conducted a single-centre retrospective study to assess the impact of post-Fontan protein-losing enteropathy on transplant-free survival. We also described resource utilisation and treatment variations among post-Fontan protein-losing enteropathy patients. Children who received care at our centre between 2009 and 2017 after the Fontan surgery were eligible. Initial admissions for the Fontan operative procedure were excluded. Demographics, hospital admissions, resource utilisation, medications and charges were reviewed. Patients were divided into two groups based on the presence of post-Fontan protein-losing enteropathy. Of the 343 patients screened, 147 met the eligibility criteria. Of these, 28 (19%) developed protein-losing enteropathy. After adjusting for follow-up duration, the protein-losing enteropathy group had higher number of encounters (2.15 ± 2.16 versus 1.47 ± 2.56, p 0.002), hospital length of stay (days) (25 ± 51.3 versus 11.4 ± 41.7, p < 0.0001) and total charges (2018US$) (388,489 ± 759,859 versus 202,725 ± 1,076,625, p < 0.0001). Encounters for patients with protein-losing enteropathy utilised more therapies. Among those with protein-losing enteropathy, use of digoxin was associated with slightly decreased odds for mortality and/or transplant (0.95, confidence interval 0.90–0.99, p 0.021). The 10-year transplant-free survival for patients with/without protein-losing enteropathy was 65.7/97.3% (p 0.002), respectively. Post-Fontan protein-losing enteropathy is associated with reduced 10-year transplant-free survival, higher resource utilisation, charges and medication use compared with the non-protein-losing enteropathy group. Practice variation among post-Fontan protein-losing-enteropathy patients is common. Further larger studies are needed to assess the impact of standardisation on the well-being of children with post-Fontan protein-losing enteropathy.