Objective: Pregnancies conceived via intracytoplasmic sperm injection (ICSI) are associated with a higher risk of fetal cardiac remodeling. The aim of this study was to evaluate whether the type of embryo transfer may affect the magnitude of fetal cardiac remodeling in pregnancies conceived via ICSI. Methods: Prospective cross-sectional study including 212 pregnancies conceived by ICSI (111 with frozen and 101 with fresh embryos) and 120 spontaneously conceived gestations. All women underwent ultrasound biometric evaluation, Doppler, and echocardiographic assessment, including evaluation of left and right atrial areas and sphericity index (SI), at 20–24 weeks of gestation. The χ<sup>2</sup> and Kruskal-Wallis H tests were used to analyze the data. Results: There was no difference in maternal characteristics, gestational age at ultrasound, Doppler, and fetal weight among the study groups. In pregnancies conceived by ICSI, left and right atrial areas were higher (p < 0.0001) and SI was lower (p < 0.0001) compared to spontaneously conceived pregnancies. Left (p = 0.004) and right (p = 0.023) atrial areas and left (p = 0.036) and right (p = 0.002) SIs were more affected in ICSI pregnancies conceived by fresh embryos. Conclusion: The risk of fetal cardiac remodeling is higher in pregnancies conceived by ICSI and independent from fetal size and Doppler. The magnitude of these changes is affected by the type of ICSI technique and is higher in pregnancies conceived by fresh embryos.