Single ventricle congenital heart disease (SV CHD) patients are at risk of morbidity and mortality between the first and second palliative surgical procedures (interstage). When these patients present acutely they often require invasive intervention. This study sought to compare the outcomes and costs of elective and emergent invasive cardiac procedures for interstage patients. Retrospective review of discharge data from The Vizient Clinical Data Base/Resource Manager™, a national health care analytics platform. The database was queried for admissions from 10/2014 to 12/2017 for children 1–6 months old with ICD-9 or ICD-10 codes for SV CHD who underwent invasive cardiac procedures. Demographics, length of stay (LOS), complication rate, in-hospital mortality and direct costs were compared between elective and emergent admissions using t test or χ², as appropriate. The three most frequently performed procedures were also compared. 871 admissions identified, with 141 (16%) emergent. Age of emergent admission was younger than elective (2.9 vs. 4 months p < 0.001). Emergent admissions including cardiac catheterization or superior cavo-pulmonary anastomosis had longer LOS (58.7 vs. 25.8 day, p < 0.001 and 54.8 vs .22.6 days, p < 0.001) and higher costs ($134,774 vs. $84,253, p = 0.013 and $158,679 vs. $81,899, p = 0.017). Emergent admissions for interstage SV CHD patients undergoing cardiac catheterization or superior cavo-pulmonary anastomosis are associated with longer LOS and higher direct costs, but with no differences in complications or mortality. These findings support aggressive interstage monitoring to minimize the need for emergent interventions for this fragile patient population.