Cardiac MRI in neonates holds promise as a tool that can provide detailed functional information in this vulnerable group. However, their small size, rapid heart rate, and inability to breath-hold, pose particular challenges that require prolonged high-contrast and high-SNR methods. Balanced-steady state free precession (SSFP) offers high SNR efficiency and excellent contrast, but is vulnerable to off-resonance effects that cause banding artifacts. This is particularly problematic in the blood-pool, where off-resonance flow artifacts severely degrade image quality. Methods: In this article, we explore active frequency stabilization, combined with image-based shimming, to achieve prolonged SSFP imaging free of banding artifacts. The method was tested using 2D multislice SSFP cine acquisitions on 18 preterm infants, and the functional measures derived were validated against phase-contrast flow assessment. Results: Significant drifts in the resonant frequency (165 ± 23Hz) were observed during 10-min SSFP examinations. However, full short-axis stacks free of banding artifacts were achieved in 16 subjects with stabilization; the cardiac output obtained revealed a mean difference of 9.0 ± 8.5% compared to phase-contrast flow measurements. Conclusion: Active frequency stabilization has enabled the use of prolonged SSFP acquisitions for neonatal cardiac imaging at 3T. The findings presented could have broader implications for other applications using prolong SSFP acquisitions. Magn Reson Med 70:776–784, 2013. © 2012 Wiley Periodicals, Inc.