Abstract Background Live cell-based assays (CBA) are considered the gold-standard methodology for detecting pathogenic antibodies targeting neural cell surface antigens. However, the adoption of these methods in clinical laboratories has been limited by their manual nature and low throughput. Here, we describe the development and validation of an automated system utilizing a live flow cytometry-based CBA to detect AQP4-IgG. Establishing AQP4-IgG serostatus is a critical component of the diagnostic criteria for Neuromyelitis optica spectrum disorders (NMOSD) as it enables the differentiation of NMOSD from Multiple Sclerosis where there may be significant clinical overlap. The accurate diagnosis of the correct disease state is vital, as the prognosis and treatment approach differ significantly for these two conditions. Two redundant systems were built that automatically receive reagents (live cells in suspension, buffers, diluents, secondary antibodies, and patients’ samples) and generate flow cytometer ready 96-well plates (each containing up to 45 serum or CSF samples tested in duplicate). Methods We assessed the analytical performance of an AQP4-IgG live flow cytometry-based CBA on these new automated systems. We measured intra- and inter-assay imprecision at three levels in 5x5 format and for end-point titer assessment, accuracy (20 positive and 20 negative sera; 5 positive and 5 negative CSF; established on the current manual assay), reference range (20 negative sera and 20 negative CSF from disease controls), analytical sensitivity (LOB and LOD) and specificity (high IgG containing serum specimens), within-plate draft (1 positive sample near the diagnostic cut-off [IgG-binding index of 2.0] that was tested across the entire plate), instrument to instrument correlation (42 positive samples/dilutions tested simultaneously on both systems), and total throughput for both CSF and Serum. Results Imprecision testing yielded the following results: Serum Intra/Inter precision level 1 (IBI = 2) CV% (current method:4.6%/20.7%), (system 1: 3.1%/18.4%), (system 2: 2.6%/22.5%), serum Intra/Inter precision level 2 (IBI=4) CV% (current method:4.9%/23.3%), (system 1: 3.2%/21.9%), (system 2: 2.6%/24.1%), and serum Intra/Inter precision level 3 (IBI =10) pos CV% (current method:6.0%/31.1%), (system 1: 3.8%/27.4%), (system 2: 4.2%/29.4%), and CSF Intra/Inter precision (IBI =2) CV% (System 1: 11.7%/16.8%), (system 2: 6.1%/10.7%). The median end-point titers for all four samples assessed matched within one end-point titer. For accuracy, 100% qualitative agreement between current and both automated systems, and titration accuracy (5 positive serums, 1 positive CSF) all matched within one titer between current and both automated systems. All reference range samples were negative. LOB/LOD in serum (Current: 0.85/1.11), (System 1: 0.82/0.95), (system 2: 0.82/0.96) and CSF (Current: 1.06/1.52), (System 1: 1.02/1.38), (system 2: 1.02/1.64) were comparable. All high IgG samples were negative. Plate drift analysis showed improved whole plate %CV: (Current:6.52%), (system 1: 4.51%), (system 2: 3.46%). Instrument to instrument comparison utilizing linear regression indicated strong agreement across the two systems (slope = 0.93 and R2= 0.95). Assessment of throughput based on real-time timings indicated a maximum output of approximately >700 patient samples per 24hrs per system. Conclusions An automated system for performing live CBAs provides equivalent to superior analytical performance compared to pre-existing manual methods with improved testing capacity.