D-serine has been implicated as a brain messenger with central roles in neural signaling and plasticity. Disrupted levels of D-serine in the brain have been associated with neurological disorders, including schizophrenia, depression and Alzheimer’s disease. Electrochemical biosensors are attractive tools for measuring real-time in vivo D-serine concentration changes. Current biosensors suffer from relatively large sizes (≥25 μm) making localized cellular measurements challenging, especially for single cell studies. In this work, a robust methodology for the fabrication of a reproducible miniaturized 10 μm D-serine detecting amperometric biosensor was developed. The miniature biosensor incorporated yeast D-amino acid oxidase immobilized on a poly-meta-phenylenediamine modified 10 μm Pt disk microelectrode. The biosensor offered a limit of detection of 0.361 μM (RSD < 10%) with high sensitivity (283 μA cm−2 mM−1, R2 = 0.983). The biosensor was stable for over four hours of continuous use, demonstrated a storage stability of four days and high analyte selectivity. Biosensor selectivity was validated with LC-MS and interferences with yeast D-amino acid oxidase were evaluated using drugs believed to stimulate D-serine release. Ex vivo D-serine measurements were made from Xenopus laevis tadpole brains, demonstrating the utility of the biosensors for measurements on living tissue. We observed that D-serine levels in the brain fluctuate with sensory experience. The biosensors were also used in vivo successfully. Taken together, this study addresses factors for successful and reproducible miniature biosensor fabrication for measuring D-serine in biological samples, for pharmacological evaluation, and for designing point of care devices.