Purpose: To compare nerve fiber layer thickness (NFLT) in patients with glaucoma measured by two versions of an analysis program utilizing optical coherence tomography (OCT) with reference to the cup-to-disk (C/D) ratio and the mean deviation (MD) score of a static visual field test. Methods: Twenty-four eyes from 24 glaucoma patients were enrolled. The NFLT was measured by OCT along a circle around the disk with the circle diameter being 1.5 times that of the disk itself. The NFLTs evaluated by the two versions A4.01 and A6.01 were compared with respect to the C/D ratio and MD score. Results: The mean NFLTs evaluated by version A6.01 were 61.2% greater than those evaluated by version A4.01 (p < 0.001). The NFLTs in all quadrants evaluated by A6.01 were also greater than those evaluated by A4.01. Both A6.01 and A4.01 showed a significant correlation with the C/D ratio and MD score. Although A6.01 showed a better correlation with the C/D ratio than A4.01, both A4.01 and A6.01 showed similarly good correlations with MD. Conclusion: The NFLTs evaluated by the two versions differed significantly with regard to some parameters. These results should be taken into account in evaluating NFLTs when utilizing OCT.