The effects of fish oil (FO) or omega-3 supplementation on cognition has been the subject of several previous clinical trials. However, the effect of different doses taken chronically on cognition in children has not been well studied. In order to address this gap in our knowledge, we conducted a randomized, double-blind, placebo-controlled clinical trial. A total of one hundred and twenty healthy, cognitively normal Thai children aged 6–12 years old consumed daily low dose FO (260 mg Docosahexaenoic acid (DHA)), high dose FO (520 mg DHA), or placebo (Soybean oil) for 12 weeks. Cognitive function was assessed using a computerized cognitive battery, including the Go/NoGo, N-Back, and Digit Span tests as well as concurrent event-related potentials (ERPs), which together measured attention, processing speed, inhibition, and memory at baseline and 12 weeks. We hypothesized that compared to placebo, the two FO groups would show improved cognitive performance and shorter ERP latencies. In total, 42, 39, and 39 participants completed each of the test (FO-A, FO-B) and placebo groups (P) allocations, respectively, and were analyzed (120 in total across the three groups). No significant differences were observed between reaction times (RTs), accuracy, or error rates for all three of the cognitive tests. The ERP measurement and analysis of brain activity during the cognitive tests showed an increase in ERP amplitude. For all cognitive tests, there was a dose-response effect of FO on ERP amplitudes. These findings indicate that fish oil intake leads to a consistent improvement in attention and cognitive processing ability measured by changes in brain activity during working and long-term memory processes. This is the first study to directly quantify such an effect through simultaneous measurement of manual and mental activity during cognitive tasks following chronic FO use in children.