Adaptive optics—optical coherence tomography (AO-OCT) is a non-invasive technique for imaging retinal vascular and structural features at cellular-level resolution. Whereas retinal blood vessel density is an important biomarker for ocular diseases, particularly glaucoma, automated blood vessel segmentation tools in AO-OCT have not yet been explored. One reason for this is that AO-OCT allows for variable input axial dimensions, which are not well accommodated by 2D-2D or 3D-3D segmentation tools. We propose a novel bidirectional long short-term memory (LSTM)-based network for 3D-2D segmentation of blood vessels within AO-OCT volumes. This technique incorporates inter-slice connectivity and allows for variable input slice numbers. We compare this proposed model to a standard 2D UNet segmentation network considering only volume projections. Furthermore, we expanded the proposed LSTM-based network with an additional UNet to evaluate how it refines network performance. We trained, validated, and tested these architectures in 177 AO-OCT volumes collected from 18 control and glaucoma subjects. The LSTM-UNet has statistically significant improvement (p < 0.05) in AUC (0.88) and recall (0.80) compared to UNet alone (0.83 and 0.70, respectively). LSTM-based approaches had longer evaluation times than the UNet alone. This study shows that a bidirectional convolutional LSTM module improves standard automated vessel segmentation in AO-OCT volumes, although with higher time cost.