Background: The proportion of intensive care unit (ICU) admissions in children that have and have not been directly caused by SARS-CoV-2 remains unclear. The aim of the study is to analyse a cohort of children admitted to the ICU with SARS-CoV-2 and determine whether the infection was the primary cause of their hospitalisation, a significant contributor, a suspected accomplice, or an incidental finding. Methods: This was a retrospective observational study of all the children admitted to the ICU with SARS-CoV-2 from March 2020 to February 2022 from the South Moravia region. The aim of the study was to assess whether the hospitalisation was likely to be directly caused by the virus (i.e., patients with acute COVID-19; the COVID group), whether the virus was a significant contributor to the hospitalisation (i.e., patients with multisystem inflammatory syndrome in children due to COVID-19; the MIS-C group), whether it may have contributed to the worsening of their underlying disease (the WORSENING group), or whether it was an incidental finding very likely unrelated to hospitalisation where SARS-CoV-2 positivity merely placed patients in the COVID-19 unit (the ISOLATION group). The groups were compared using a series of secondary outcomes. Results: The study population represented 150 paediatric ICU cases (age 8.6; IQR 3.5–13.3 years), with 66.7% being male. The COVID group represented 32.7% of cases (49/150); MIS-C, 30% (45/150); WORSENING, 14.7% (22/150); and ISOLATION, 22.7% (34/150). The median length of hospitalisation was found for the MIS-C group (11 days; 9 days in the ICU), the COVID group (6 days; five days in the ICU), WORSENING group (4.5 days; 4.5 days in the ICU) and the ISOLATION group (5.5 days; 3.5 days in the ICU), where the difference was significant (p < 0.001). Asymptomatic and mild cases were most common in the WORSENING (36.4% and 63.6%) and ISOLATION (52.9% and 44.1%) groups. Severe and critical cases were only present in the COVID (6.1% and 12.2%) and MIS-C (4.4% and 11.1%) groups; the severity difference was significant (p < 0.001). The groups did not differ significantly in the proportion of complete recovery and short- and long-term sequelae (p = 0.09).