Viral infection of the central nervous system (CNS) results in a rapid influx of bone marrow (BM)-derived monocytes/macrophages, that ultimately induce fatal pathology in the mouse. Whilst these cells are derived from the BM, little is known about the kinetic and migratory events that mobilise BM monocytes and their progenitors in response to CNS infection. In this study we conducted comprehensive mapping of the murine haemopoietic system in the BM using high-dimensional single cell flow and mass cytometry (CyTOF), and a 10-laser 30-parameter BD LSR-II platform. Initially, we used this approach to refine the identification of myeloid developmental intermediates involved in monopoiesis and granulopoiesis, during steady state and inflammation. Additionally we examined the expression of the transcription factor IRF8 across the haematopoietic system and its role in instructing myeloid developmental trajectories. During viral encephalitis, we found a reorganisation of cellular outputs to favour monocyte production, resulting in activation and expansion of monocytes and monocyte progenitors, with increased proliferation of mature and progenitor populations. In addition, we observed compensatory downregulation of B-cell lymphopoiesis, and modification of granulopoiesis in the BM, favouring monocyte expansion. The upregulation of the interferon (IFN)-inducible marker SCA-1 on specific lineages suggested a role for IFN signalling, and implicates IFN-gamma (IFN-g) producing NK and T-cells in the BM in this process. As such, antibody blockade of IFN-g resulted in a reduction of monocyte-drived pathology, associated with improved clinical outcomes. In this study we have used high-dimensional cytometry approaches, and have characterized modifications to the haematopoietic lineage during viral encephalitis that favour production of pathogenic monocytes.