To evaluate the clinical characteristics associated with chronic pachychoroid neovasculopathy (PNV) accompanying recalcitrant intraretinal cysts.This is a retrospective, single-center, case-series study involving 20 eyes of 18 patients with PNV who did not respond to bevacizumab or ranibizumab and had to switch to aflibercept. Optical coherence tomography images were assessed before and after switching of intravitreal injection drug.The intraretinal cysts involved the outer nuclear layer and inner nuclear layer in 15 patients (75.0%), and involved only the inner nuclear layer in five patients (25.0%). All participants showed retinal pigment epithelium atrophy and outer retinal layer defect including external limiting membrane defect co-localized to the intraretinal cystic lesion. With the initial injection, bevacizumab and ranibizumab injections did not show a significant decrease in choroidal thickness (CT). Twenty (100.0%) patients showed poor response of intraretinal cyst response (IRCR). After a switch to aflibercept, IRCR was good in 17 (85.0%) patients and poor in three (15.0%) patients. Reduction of CT was great in aflibercept injections (from 229.0 μm to 204.0 μm, median, p < 0.001). Best-corrected visual acuity did not show significant improvement before or after switching drugs.Intravitreal aflibercept injections were more effective in the reduction of CT and IRCR than bevacizumab and ranibizumab injections. The primary source of the intraretinal cyst fluid could be from the choroid.