Vitamin D and calcium are essential nutrients with a range of biological effects of public health relevance. This study aimed to validate a short food frequency questionnaire (SFFQ) against a three-day food record (3D record), assessing the intake of vitamin D and calcium in Swedish children during wintertime. In a double-blinded, randomized food-based intervention study on the effect of feeding different daily doses of vitamin D supplement to 5–7-year-old children (n = 85), 79 (93%) participants completed SFFQ1 at baseline and SFFQ2 after the intervention, and 72 were informed to fill in a 3D record. The 28 (39%) children who completed the 3D record were included in this validation study. The baseline level of serum-25 hydroxy vitamin D [S-25(OH)D] was used as a biomarker. The correlation between all three instruments were moderate to strong. SFFQ2 and the 3D record correlated moderately to S-25(OH)D. Bland-Altman analysis showed that SFFQ2 overestimated vitamin D intake by on average 0.6 μg/day, (limits of agreement (LOA) 5.7 and −4.6 μg/day), whereas the intake of calcium was underestimated by on average 29 mg/day, (LOA 808 and −865 mg/day). Finally, the validity coefficient calculated for vitamin D using the method of triad was high (0.75). In conclusion, this SFFQ, assessed by a dietician, is a valid tool to assess dietary vitamin D and calcium intake in groups of young children.