The properties of graphene oxide (GO) have received much attention and been applied to the exploration of potential applications in disease-related diagnostics and non-invasive therapy. One application, photodynamic therapy (PDT), involves the killing of cancer cells where singlet oxygen is generated with light irradiation of the appropriate wavelength. In this work, three new BODIPY derivatives (13–15), decorated with carbohydrate moieties for active targeting and branched ethylene glycol for biocompatibility, and their GO based nanocarriers were designed to study the singlet oxygen production and PDT efficiency. First, BODIPYs were prepared, followed by the fabrication of GO layers with BODIPY dyes via a non-covalent method. Detailed characterizations of the materials were carried out with mass spectrometry, FT-IR spectroscopy, 1H NMR, 13C NMR, elemental analysis, Raman spectroscopies, EDX analysis and TEM and AFM microscopies. The efficiency of singlet oxygen generation in organic and water-based solutions was determined by photobleaching with 1,3-diphenylisobenzofuran (DPBF) and 9,10-anthracenediyl-bis(methylene)dimalonic acid (ABDA), respectively. The results in in vitro PDT analysis against K562 human cancer cells indicate the prepared materials are highly promising in PDT anticancer therapy and the IC50 values of GO loaded BODIPY derivatives bearing heavy atoms, GO-14 and GO-15, were calculated as 40.59 nM and 39.21 nM, respectively.