Creatine transporter deficiency (CTD) is a rare X-linked disorder resulting from pathogenic variants in the SLC6A8 gene. These variants cause cognitive disability through by disrupting energy metabolism as well as other mechanism within the central nervous system. In order to identify potential plasmatic biomarkers in relation with the CNS phenotype of male CTD patients, a shotgun proteomic analysis of plasma samples from male CTD patients with confirmed SLC6A8 pathogenic variants was performed with a high-resolution tandem mass spectrometer. Proteins from the samples were proteolyzed in technical duplicate. The resulting peptides were characterized by tandem mass spectrometry with an Exploris 480 instrument (Thermo). Files .raw.quant were obtained with DIA-NN. The dataset comprises the list of 24 raw files (12 samples analyzed in technical duplicates), the 24 raw quant files, and the DIA-NN outputs (list of protein groups and their abundances, list of precursors and their intensities). This dataset is associated with the scientific manuscript entitled "Proteomic analysis reveals blood biomarkers associated with brain dysfunction in creatine transporter deficiency" authored by Clémence Disdier, Rania Harati, Aurore Curie, Anne-Cécile Guyot, Jean Armengaud, Nathalie Dufay, David Cheillan, Farha Gheurbi, Marion Buchy, Rifat Hamoudi, and Aloise Mabondzo, submitted to publication.