Invasive meningococcal disease (IMD) remains a major public health challenge due to its rapid progression, which may lead to severe sequelae or death in children and adolescents. Published data on IMD sequelae are limited in Greece and many EU countries. In the present study, patients under 16 years of age with IMD were retrospectively identified from the files of the Hellenic National Meningitis Reference Laboratory (HNML) from 2010–2020, and their medical records were tracked from the corresponding hospitals. Demographic, clinical, and microbiological data were recorded for each case. A total of 161 patients younger than 16 years of age admitted to nine hospitals across the country were identified. Of those, 91 (56.5%) records were found. The patients’ median age was 36 months (range 22 days to 16 years old); 37.4% presented with meningitis, 36.2% with both septicemia and meningitis, and 26.4% only with septicemia. The mortality rate was 5.5% and was significantly associated with septicemia, abnormal platelet count at presentation, ICU admission, and coagulation disorders, while sequelae were detected in 16.9% of patients upon discharge. Neisseria meningitidis serogroup B (MenB) was the most predominant (77%); of these, 269 cc was identified (36.8%). This is the first study on unfavorable sequelae and mortality due to IMD performed in Greece.