The Objective of our study was to investigate the influence of dietary (dGDM) and insulin-dependent (iGDM) gestational diabetes (GDM) on BDNF blood levels of corresponding maternal-neonatal pairs and compare them to pregnancies unaffected by GDM. Blood samples from 293 maternal-neonatal pairs were analyzed. Statistical analysis was performed using multiple regression analysis for association of log-transformed maternal and neonatal BDNF levels in relation to GDM, gestational age, neonatal sex, and mode of delivery. This was followed by a 2:1 matching of healthy and diabetic pairs. Maternal and neonatal BDNF levels were lowest in the iGDM group, followed by the dGDM group and healthy controls (maternal: healthy 665 ± 562 (26–2343) pg/mL vs. dGDM 593 ± 446 (25–1522) pg/mL vs. iGDM 541 ± 446 (68–2184) pg/mL; neonate: healthy 541 ± 464 (9.5–2802) pg/mL vs. dGDM 375 ± 342 (1–1491) pg/mL vs. iGDM 330 ± 326 (47–1384) pg/mL). After multiple regression analysis and additional 2:1 matching neonatal log-BDNF was significantly lower (−152.05 pg/mL, p = 0.027) in neonates of mothers with GDM compared to healthy pairs; maternal log-BDNF was also lower (−79.6 pg/mL), but did not reach significance. Our study is the first to analyze BDNF in matched maternal-neonatal pairs of GDM patients compared to a metabolically unaffected control group.