Aim: To describe the fundus autofluorescence (FAF) characteristics of choroidal neovascularisation (CNV) associated with pathological myopia (PM), and their modification after photodynamic therapy (PDT). Design: Open-label, prospective, interventional case series. Methods: Forty-two patients affected by subfoveal CNV in PM underwent PDT with a 24-month follow-up. Each patient underwent an ophthalmological examination every 3 months, including FAF and fluorescein angiography. FAF distribution was qualitatively evaluated at the CNV site, around the CNV and outside the area affected by CNV. Results: CNV at baseline showed a high FAF signal with uniform distribution, or with some spots of low FAF internally, in 64% and 36% of cases, respectively. At the 3-month control after PDT, the CNV retained the same response, but a round halo of increased signal extending beyond the site of the PDT application was detectable around the CNV. At the end of the follow-up, a high or a low FAF signal was detected in 40% and 60% of cases, respectively. Conclusion: CNV secondary to PM shows a specific, high signal, FAF pattern. A round halo of increased FAF signal surrounding the CNV was detectable after PDT application, whereas a FAF signal progressive reduction was visible at and around the CNV site from the sixth month. A high FAF signal at the CNV site is associated with an improved visual acuity outcome at the 2-year follow-up. Further studies to correlate the morphological and functional features are advisable, especially by means of microperimetric analyses and with a longer-term follow-up.