Ebola virus (EBOV) disease is a complex zoonosis that is highly virulent in humans and has caused many deaths. Highly sensitive detection of EBOV is of great importance for early-stage diagnosis for increasing the probability of survival. Herein, we established a cellular-beacon-mediated counting strategy for an ultrasensitive EBOV assay on a micromagnetic platform. The detection platform, which was assisted by on-demand magnetic-field manipulation, showed high integration and enhanced complex-sample pretreatment by magnetophoretic separation and continuous-flow washing. Cellular beacons (i.e., fluorescent cells) with superior optical properties were used as reporters, and each cellular beacon was used as a fluorescent tracking unit to quantify EBOV by counting the numbers of individual fluorescent signals on the micromagnetic platform. This method achieves high sensitivity with a detection limit as low as 2.6 pg/mL, and the detection limit shows little difference in a complex matrix. In addition, it has excellent specificity and good reproducibility. These results indicate that this method proposes an ultrasensitive detection strategy for early diagnosis of the disease.