Nonsymbolic numerical comparison task performance (whereby a participant judges which of two groups of objects is numerically larger) is thought to index the efficiency of neural systems supporting numerical magnitude perception, and performance on such tasks has been related to individual differences in math competency. However, a growing body of research suggests task performance is heavily influenced by visual parameters of the stimuli (e.g. surface area and dot size of object sets) such that the correlation with math is driven by performance on trials in which number is incongruent with visual cues. Almost nothing is currently known about whether the neural correlates of nonsymbolic magnitude comparison are also affected by visual congruency. To investigate this issue, we used functional magnetic resonance imaging (fMRI) to analyze neural activity during a nonsymbolic comparison task as a function of visual congruency in a sample of typically developing high school students (n = 36). Further, we investigated the relation to math competency as measured by the preliminary scholastic aptitude test (PSAT) in 10th grade. Our results indicate that neural activity was modulated by the ratio of the dot sets being compared in brain regions previously shown to exhibit an effect of ratio (i.e. left anterior cingulate, left precentral gyrus, left intraparietal sulcus, and right superior parietal lobe) when calculated from the average of congruent and incongruent trials, as it is in most studies, and that the effect of ratio within those regions did not differ as a function of congruency condition. However, there were significant differences in other regions in overall task-related activation, as opposed to the neural ratio effect, when congruent and incongruent conditions were contrasted at the whole-brain level. Math competency negatively correlated with ratio-dependent neural response in the left insula across congruency conditions and showed distinct correlations when split across conditions. There was a positive correlation between math competency in the right supramarginal gyrus during congruent trials and a negative correlation in the left angular gyrus during incongruent trials. Together, these findings support the idea that performance on the nonsymbolic comparison task relates to math competency and ratio-dependent neural activity does not differ by congruency condition. With regards to math competency, congruent and incongruent trials showed distinct relations between math competency and individual differences in ratio-dependent neural activity.