A 4-component meningococcus group B vaccine (4CMenB) is the only vaccine in use to prevent group B invasive meningococcal disease in young children, but no matched controlled studies have evaluated it. To determine the association between receipt of 4CMenB and invasive group B meningococcal disease. Matched incidence density case-control study. Patients presenting from October 2014 to March 2019 were ascertained, with follow-up until death or discharge (last follow-up in June 2019) in 31 pediatric services in Portugal. Children and adolescent residents in Portugal with laboratory-confirmed invasive meningococcal disease were included. Controls, usually 2 per case, with unrelated conditions who were at the same hospital at the same time were matched for sex, age, and residence. Immunization with 4CMenB, ascertained from the national database (2-4 doses are recommended, depending on age). The primary outcome was group B invasive meningococcal disease in fully vaccinated cases compared with controls. The secondary outcomes were all serogroup invasive meningococcal disease in fully vaccinated cases compared with controls and group B and all serogroup invasive meningococcal disease in cases compared with controls who received at least 1 vaccine dose. Of 117 patients with invasive meningococcal disease, 98 were eligible for inclusion and 82 had group B invasive meningococcal disease; 69 were old enough to have been fully vaccinated and considered protected. Among these 69 cases, the median (interquartile range) age was 24 (4.5-196) months, 42 were male, and the median (interquartile range) duration of hospitalization was 8 (0-86) days. Five of 69 cases (7.2%) and 33 of 142 controls (23.1%) were fully vaccinated (difference, -16.0% [95% CI, -26.3% to -5.7%]; odds ratio [OR], 0.21 [95% CI, 0.08-0.55]). For all serogroup invasive meningococcal disease, 6 of 85 cases (7.1%) and 39 of 175 controls (22.3%) were fully vaccinated (difference, -15.2% [95% CI, -24.3% to -6.1%]; OR, 0.22 [95% CI, 0.09-0.53]). For group B disease, 8 of 82 cases (9.8%) and 50 of 168 controls (29.8%) received at least 1 vaccine dose (difference, -20.0% [95% CI, -30.3% to -9.7%]; OR, 0.18 [95% CI, 0.08-0.44]) and for all serogroup invasive meningococcal disease, 11 of 98 cases (11.2%) and 61 of 201 controls (30.3%) received at least 1 vaccine dose (difference, -19.1% [95% CI, -28.8% to -9.5%]; OR, 0.23 [95% CI, 0.11-0.49]). During the first 5 years of vaccine availability in Portugal, vaccination with 4CMenB was less likely among children who developed invasive meningococcal disease compared with matched controls without invasive meningococcal disease. These findings may help inform the use of the 4CMenB vaccine in clinical practice. ISRCTN Identifier: ISRCTN10901628.