Polyetheretherketone (PEEK), due to its excellent mechanical and physico-chemical parameters, is an attractive substitute for hard tissues in orthopedic applications. However, PEEK is hydrophobic and lacks surface-active functional groups promoting cell adhesion. Therefore, the PEEK surface must be modified in order to improve its cytocompatibility. In this work, extreme ultraviolet (EUV) radiation and two low-temperature, EUV induced, oxygen and nitrogen plasmas were used for surface modification of polyetheretherketone. Polymer samples were irradiated with 100, 150, and 200 pulses at a 10 Hz repetition rate. The physical and chemical properties of EUV and plasma modified PEEK surfaces, such as changes of the surface topography, chemical composition, and wettability, were examined using atomic force microscopy (AFM), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and goniometry. The human osteoblast-like MG63 cells were used for the analysis of cell viability and cell adhesion on all modified PEEK surfaces. EUV radiation and two types of plasma treatment led to significant changes in surface topography of PEEK, increasing surface roughness and formation of conical structures. Additionally, significant changes in the chemical composition were found and were manifested with the appearance of new functional groups, incorporation of nitrogen atoms up to ~12.3 at.% (when modified in the presence of nitrogen), and doubling the oxygen content up to ~25.7 at.% (when modified in the presence of oxygen), compared to non-modified PEEK. All chemically and physically changed surfaces demonstrated cyto-compatible and non-cytotoxic properties, an enhancement of MG63 cell adhesion was also observed.