The performance of platelet (PLT) counting in thrombocytopenic samples is crucial for transfusion decisions. We compared PLT counting and its reproducibility between Mindray BC-6800Plus (BC-6800P, Mindray, Shenzhen, China) and Sysmex XN-9000 (XN, Sysmex, Kobe, Japan), especially focused on thrombocytopenic samples. We analyzed the correlation and agreement of PLT-I channels in both analyzers and BC-6800P PLT-O mode and XN PLT-F channel in 516 samples regarding PLT counts. Ten thrombocytopenic samples (≤2.0 × 109/L by XN PLT-F) were measured 10 times to investigate the reproducibility with the desirable precision criterion, 7.6%. The correlation of BC-6800P PLT-I and XN PLT-I was arranged moderate to very high; but the correlation of BC-6800P PLT-O and XN PLT-F was arranged high to very high. Both BC-6800P PLT-I vs. XN PLT-I and BC-6800P PLT-O vs. XN PLT-F showed very good agreement (κ = 0.93 and κ = 0.94). In 41 discordant samples between BC-6800P PLT-O and XN PLT-F at transfusion thresholds, BC-6800P PLT-O showed higher PLT counts than XN-PLT-F, except the one case. BC-6800P PLT-O exceeded the precision criterion in one of 10 samples; but XN PLT-F exceeded it in six of 10 samples. BC-6800P would be a reliable option for PLT counting in thrombocytopenic samples with good reproducibility.