In hospitalized children, SARS‐CoV‐2 infection can present as either a primary reason for admission (patients admitted for COVID‐19) or an incidental finding during follow‐up (patients admitted with COVID‐19). We conducted a nested case‐control study within a cohort of pediatric patients with confirmed SARS‐CoV‐2 infection, to investigate the concentration of plasma nucleocapsid antigen (N‐Ag) in children admitted for COVID‐19 or with COVID‐19. While reverse transcriptase polymerase chain reaction Ct values in nasopharyngeal swab were similar between the two groups, children admitted for COVID‐19 had a higher rate of detectable N‐Ag (12/18 (60.7%) versus 6/18 (33.3%), p = 0.0455) and a higher concentration of N‐Ag (medians: 19.51 g/mL vs. 1.08 pg/mL, p = 0.0105). In children hospitalized for COVID‐19, the youngest had higher concentration of N‐Ag (r = −0.74, p = 0.0004). We also observed a lower prevalence of detectable spike antibodies in children hospitalized for COVID‐19 compared to those hospitalized for other medical reasons (3/15 [20%] vs. 13/16 [81.25%], respectively, p = < 0.0011), but similar rates of IgG nucleocapsid antibodies (5/14 [35.7%] vs. 6/17 [35.3%], respectively, p = 0.99). Our findings indicate that N‐Ag is associated with COVID‐19‐related hospitalizations in pediatric patients, and less frequently detected in children tested positive for SARS‐CoV‐2 but hospitalized for another medical reason. Further studies are needed to confirm the value of N‐Ag in identifying COVID‐19 disease infections in which SARS‐CoV‐2 is the main pathogen responsible for symptoms.