Introduction: This cross-sectional study investigated the rate of congenital and neonatal malaria infections in patients attending our hospital. Methodology: Thick and thin blood films of 288 neonates admitted in the Special Care Baby Unit of Jos University Teaching Hospital, Nigeria, were examined microscopically for malaria parasites. Babies' and mothers' demographic and clinical data were analyzed. Results: Of 288 blood samples examined, 160 (55.6%) were from males, 115 (39.9%) were from babies 0 to 7 days old, and 173 (60.1%) were from babies 8 to 28 days old. In total, 91 (31.6%) babies had malaria parasitaemia, of whom 49 (53.8%) were males. Malaria was significantly higher in babies 8 to 28 days old (p<0.001) and was independent of gender (p=0.692). Prevalence rates for congenital and neonatal malaria were 6.9% and 24.7% respectively. Clinical presentations on admission included fever, cough, pallor, jaundice, and inability to suck. A total of 145 (50.3%) babies had symptoms of malaria, of whom 56 (61.5%) had malaria parasitaemia. Symptoms of malaria were present in 35 (12.2%) babies of 59 (20.5%) mothers who had symptoms of malaria during pregnancy. Ten (11.0%) of these neonates had malaria parasitaemia, of whom 4 (0.4%) were 0 to -7days old. Plasmodium falciparum was the only specie identified. No mortality was recorded against malaria-infected babies. Conclusion: High prevalence of malaria in these neonates calls for high index of suspicion. Inclusion of malaria parasite test in the routine battery of tests for babies presenting with clinical signs and symptoms of neonatal infections is recommended.