Lower proportions of n-3 PUFAs have been observed in neonates born to diabetic mothers. We aimed to investigate the association between DHA and EPA supplementation during pregnancy complicated with type 1 diabetes on concentration and proportion of fatty acids in maternal and foetal blood. We conducted a prospective randomized, single-blinded, placebo-controlled trial of 111 eligible pregnant women with type 1 diabetes and presented the results of 84 (intervention arm and control arm comprised 42 participants each) of them who successfully finished the trial in an academic hospital. The initiation of EPA and DHA supplementation or placebo started at randomization visit on gestational week 11–12. Blood samples were taken on the first (screening) visit to the clinic (1st trimester, between 8th and 10th gestational week, GW), then in the second trimester (19–24th GW) and third trimester (30th–33rd GW). On the delivery day, a blood sample was taken on fasting just before birth. The umbilical vein blood sample was taken shortly after the delivery. We found a significant increase in the intervention group when compared the first and the third trimester for n-3 PUFAs concentration, 4.3 mg/L (3.3–7.6): 10.0 mg/L (7.1–13.7), p < .001. In the intervention group, the concentration of DHA in maternal vein serum was 11.4 mg/L (7.7–17.5), and in umbilical vein serum, it was 5.1 mg/L (3.0–7.7), which was significantly higher than that in the control group, maternal vein serum: median 9.2 mg/L(6.0–12.3), p = .03 and umbilical vein serum: median 3.4 mg/L (2.1–5.6), p = .009. The increased weight gain in pregnancy and concentration and proportions of DHA, n-3 PUFAs with a decreased proportion of AA, n-6 PUFAs, and AA/DHA ratio in maternal and umbilical vein serum summarize the effect of supplementation with EPA and DHA.