This study aimed to explore the spatial numerical association of response codes (SNARC), the flanker, and the numerical distance effects in children with mathematical difficulties. From a sample of 720 third, fourth, and fifth graders, 60 children were selected and divided into the following three groups: typically developing children (TD; n = 29), children with mathematical difficulties only (MD only; n = 21), and children with mathematical and reading difficulties (MD+RD; n = 10). Children were tested with a numerical Eriksen task that was built to assess SNARC, numerical distance, and flanker (first and second order congruency) effects. Children with MD only showed stronger SNARC and second order congruency effects than did TD children, whereas the numerical distance effects were similar across the three groups. Finally, the first order congruency effect was associated with reading difficulties. These results showed that children with mathematical difficulties with or without reading difficulties were globally more impaired when spatial incompatibilities were presented.