Background Nutrient deficiencies during pregnancy may affect offspring development. We aim to examine the association between prenatal vitamin B12 intake and children’s cognitive development. Methods A total of 5151 mother–child pairs from the Czech part of ELSPAC study were included in the analysis. Dietary information was obtained during pregnancy using food frequency questionnaire. Parents reported on their child’s speech and language development at 18 months, 3, 5 and 7 years. Intelligence quotient (IQ) was measured at 8 years in subcohort of 854 children. Results Children of mothers with higher vitamin B12 intake demonstrated higher scores in language (B = 0.20, 95% CI 0.06, 0.34) and talking and understanding (B = 2.39, 95% CI 0.97, 3.80) in a fully adjusted model at 18 months. Additionally, they were more likely to get maximum points in the intelligibility test at age 3 (OR = 1.05, 95% CI 1.01, 1.09) in unadjusted model, however, not in fully adjusted model. We found a positive effect of higher vitamin B12 intake on verbal IQ (B = 1.08, 95% CI 0.09, 2.08). Conclusions We identified consistent associations between prenatal vitamin B12 intake and children’s cognitive development. The results suggest that inadequate vitamin B12 during pregnancy may negatively affect children’s cognitive development, particularly in speech and language.