Poor diet quality may impair academic achievement in children, but such evidence is limited. Therefore, we investigated the associations of healthy diet in Grade 1 assessed by Mediterranean Diet Score (MDS), Baltic Sea Diet Score (BSDS), and Finnish Children Healthy Eating Index (FCHEI) with academic achievement in Grades 1-3 in children. The participants were 161 Finnish children who were 6-8years old in Grade 1 and attended in a large ongoing physical activity and dietary intervention study. Dietary factors were assessed using 4-day food records, and MDS, BSDS, and FCHEI were calculated. Academic achievement was assessed by reading fluency, reading comprehension, and arithmetic skill tests. The data were analyzed using linear regression analysis and analysis of covariance adjusted for age, sex, parental education, household income, body fat percentage, physical activity, the PANIC Study group, and total energy intake. MDS was positively associated with reading comprehension in Grade 3 (standardized regression coefficient β=0.167, P=0.032). BSDS was positively associated with reading fluency in Grades 2-3 and reading comprehension in Grades 1-3 (β=0.161-0.274, P<0.05). FCHEI was positively related to reading fluency in Grades 1-2 and reading comprehension in Grades 1-3 (β=0.190-0.344, P<0.05). Children in the highest third of BSDS and FCHEI had better reading fluency and reading comprehension in Grades 1-3 than children in the lowest third (P<0.05). None of the diet scores was associated with arithmetic skills. Healthier diet assessed by BSDS or FCHEI in Grade 1 was associated with better reading skills, but not with arithmetic skills, among children in Grades 1-3. Long-term intervention studies are needed to investigate the effects of improvements in diet quality on academic achievement among children. ClinicalTrials.gov Identifier: NCT01803776.