ABSTRACT Due to the continuous rise in global incidence and severity of invasive fungal infections (IFIs), particularly among immunocompromised and immunodeficient patients, there is an urgent demand for swift and accurate fungal pathogen diagnosis. Therefore, the need for fungal‐specific positron emission tomography (PET) imaging agents that can detect the infection in the early stages is increasing. Cellobiose, a disaccharide, is readily metabolized by fungal pathogens such as Aspergillus species. Recently, our group reported fluorine‐18 labeled cellobiose, 2‐deoxy‐2‐[ 18 F]fluorocellobiose ([ 18 F]FCB), for specific imaging of Aspergillus infection. The positive imaging findings with very low background signal on delayed imaging make this ligand a promising fungal‐specific imaging ligand. Inspired by this result, the decision was made to automate the radiolabeling procedure for better reproducibility and to facilitate clinical translation. A Trasis AllInOne (Trasis AIO) automated module was used for this purpose. The reagent vials contain commercially available 2‐deoxy‐2‐[ 18 F]fluoroglucose ([ 18 F]FDG), glucose‐1‐phosphate, and enzyme (cellobiose phosphorylase). A Sep‐Pak cartridge was used to purify the tracer. The overall radiochemical yield was 50%–70% ( n = 6, decay corrected) in 75‐min synthesis time with a radiochemical purity of > 98%. This is a highly reliable protocol to produce current good manufacturing practice (cGMP)–compliant [ 18 F]FCB for clinical PET imaging.