We investigated the relationship between the peripapillary retinal nerve fiber layer and peripapillary retinal thickness in patients with diabetic macular edema. Fifty eyes (group I) with non-proliferative diabetic retinopathy and diabetic macular edema receiving intravitreal anti-VEGF injection, and 90 eyes (group II) without diabetic macular edema were included in this case-control study. The peripapillary retinal nerve fiber layer thickness, peripapillary retinal thickness, and a new retinal nerve fiber layer index using a modeled relationship between the two parameters were evaluated with spectral-domain optical coherence tomography, at baseline and at the 6-month follow-up. In group I, the peripapillary retinal nerve fiber layer thickness decreased from 126.4 μm at baseline to 117.6 μm at 6 months (p < 0.001), while the peripapillary retinal thickness decreased from 376.0 μm at baseline to 359.6 μm at 6 months (p < 0.001) after intravitreal anti-VEGF injection. In group II, however, both the parameters remained stable at the 6-month follow-up (100.7 to 102.1 μm and 311.1 to 316.2 μm, respectively, and all p > 0.01). Analysis with the new index to adjust for retinal edema showed no significant change from baseline to 6 months in both groups (p = 0.593 and p = 0.101, respectively). The peripapillary retinal nerve fiber layer thickness is strongly affected by the peripapillary retinal thickness. Therefore, the measured changes in peripapillary retinal nerve fiber layer thickness may not represent the real gain or loss of the retinal nerve fiber layer. Therefore, the new retinal nerve fiber layer index, which corrects for the component of macula edema, could be a better means of assessing the changes of peripapillary retinal nerve fiber layer thickness in patients with diabetic macular edema.