This study aimed to investigate the differences between images obtained by optical coherence tomography angiography (OCTA) with those from immunohistochemical labeling of laser-induced choroidal neovascularization (CNV) in a mouse model. CNV was induced by laser photocoagulation (GYC-2000, NIDEK; wavelength 532 nm) in the left eyes of 10 female C57BL/6J mice aged 6 weeks. The laser parameters included a 100-μm spot, 100-ms pulse duration and 200-mW incident power to rupture Bruch's membrane. OCT and OCTA CNV images were obtained using the RS-3000 Advance (NIDEK) 5 days post-laser photocoagulation. After OCTA imaging, the isolated choroid/retinal pigment epithelium complexes were fluorescently labeled with CD31 (an endothelial cell marker), platelet-derived growth factor receptor β (PDGFRβ, a pericyte-like scaffold marker), α-smooth muscle actin (α-SMA) and collagen I. Area measurements of the lesions obtained by enface OCTA were compared with immunolabeled CD31+ CNV lesions in choroid flat-mounts. We also examined structural correlations between the PDGFRβ+ pericyte-like scaffold and OCTA images. Laser-induced CNV was clearly detected by enface OCTA, appearing as a hyperflow lesion surrounded by a dark halo. Area measurements of the CNV lesion by immunolabeling were significantly larger than those obtained by enface OCTA (p = 0.006). The CNV lesion beneath the periphery of the pericyte-like scaffold was not clearly visible by enface OCTA due to the dark halo; however, the lesion was detectable as blood flow by cross-sectional OCTA and was also highly labeled by CD31. The periphery of the pericyte-like scaffold appeared to develop into subretinal fibrosis and this region was rich in myofibroblasts. Enface OCTA was unable to detect the entire area of laser-induced CNV in mice, with an undetectable portion located beneath the fibrotic periphery of the pericyte-like scaffold. Due to this OCTA fibrosis artifact, OCTA imaging has limited potential for accurately estimating CNV lesions.