Sub-optimal maternal nutrition during perinatal development of her offspring can affect brain development and cognitive functions in later life. However, the consistency of effects and the causes of variation among experimental studies are not well understood. We performed a systematic search for relevant publications and selected experimental studies on rats for a meta-analysis. We extracted and analysed the differences in behavioural measures of cognition between animals subjected to inadequate nutrition during gestation and/or lactation and animals receiving control treatments. Overall, our results confirmed that cognition was indeed negatively affected by early malnutrition, but it depended on the type of learning/memory. Using meta-regression analysis, we compared the different types of behavioural tests used to measure cognition so that we were able to identify that aversive learning was less severely impaired than appetitive learning. The outcomes of our study may provide some new insights into the conflicting literature on early nutritional effects on cognition.