To analyze the clinical characteristics, trends in hospitalization and health care resource utilization of pediatric patients with cyclical vomiting syndrome (CVS). We analyzed the latest 5 Healthcare Cost and Utilization Project-Kids Inpatient Database (HCUP-KID) datasets including years 2003, 2006, 2009, 2012 and 2016 for patients aged 1-20 years with a primary diagnosis of CVS and were compared with Age/gender-matched controls for comorbidities, clinical outcomes, and healthcare resource utilization. A total of 12,396 CVS-related hospitalizations were analyzed. The mean age of CVS patients was 10.4 ± 6.7 years. CVS was associated with dysautonomia (OR: 12.1; CI: 7.0 to 20.8), dyspepsia (OR: 11.9; CI: 8.8 to 16.03), gastroesophageal reflux disease (OR: 6.9; Confidence Interval (CI): 6.4 to 7.5), migraine headaches (OR: 6.8; CI: 5.9 to 7.7) and irritable bowel syndrome (OR: 2.08; CI: 1.2 to 4.3) (all < 0.001). CVS was also associated with increased cannabis use (OR: 5.26, 4.6 to 5.9; < 0.001), anxiety disorder (OR: 3.9; CI: 3.5 to 4.4) and stress reaction (OR: 3.6; CI: 2.06 to 6.3), < 0.001. Mean CVS-related hospitalization costs (inflation adjusted) more than doubled from $3199 in 2003 to $6721 in 2016, incurring $84 million/year in total costs. Hospitalized CVS patients have increased prevalence of DGBIs, dysautonomia, psychiatric conditions and cannabis use compared to non-CVS controls. CVS-related hospitalizations in U.S. is associated with increasing health care costs. Better management of CVS and comorbid conditions is warranted to reduce health care costs and improve outcomes.