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Background/aims To compare fluctuations of central subfield retinal thickness (CSRT) in patients with neovascular age-related macular degeneration undergoing ranibizumab pro re nata versus aflibercept bimonthly treatment in a prospective 12 month, phase IV, randomised, multicentre study.Methods Ranibizumab was administered according to best-corrected visual acuity (BCVA) and/or disease activity detected on spectral domain optical coherence tomography. Aflibercept was administered at three initial monthly visits followed by bimonthly treatment. CSRT stability was evaluated between months 3 and 6. CSRT stability was compared between groups and correlated with functional outcomes at month 12.Results Fluctuations of CSRT showed a least-squares (LS) mean (95% CI) difference of −4.12 (−10.22 to 1.98) µm between ranibizumab (25.16 (20.09 to 30.24) µm) and aflibercept groups (29.28 (24.14 to 34.43) µm) (p=0.1850). A predefined analysis of retinal stability, adjusted for baseline CSRT, showed a LS mean (95% CI) difference of −6.53 (−12.47 to −0.58 µm) in favour of ranibizumab (23.53 (18.58 to 28.49) µm) versus aflibercept (30.06 (25.04 to 35.07) µm) (p=0.0315). Pearson’s correlation coefficient demonstrated no correlation between the mean amplitude of CSRT fluctuation between months 3 and 6, and BCVA at month 12 (r = −0.0888). Adverse event rates were low.Conclusions Numerical differences in retinal thickness fluctuations between months 3 and 6 were detected between treatment regimens. While the presence of fluctuations has previously been shown to have a negative impact on functional outcomes, our data showed no correlation between the mean amplitude of fluctuations and functional outcomes at month 12.