In light of an increasing awareness of the presence of bone marrow (BM)‐derived macrophages in the normal cornea and their uncertain role in corneal diseases, it is important that the turnover rate of these resident immune cells be established. The baseline density and distribution of macrophages in the corneal stroma was investigated in Cx3cr1^gfp transgenic mice in which all monocyte‐derived cells express enhanced green fluorescent protein (eGFP). To quantify turnover, BM‐derived cells from transgenic eGFP mice were transplanted into whole‐body irradiated wild‐type recipients. Additionally, wild‐type BM‐derived cells were injected into irradiated Cx3cr1^+/gfp recipients, creating reverse chimeras. At 2, 4 and 8 weeks post‐reconstitution, the number of eGFP⁺ cells in each corneal whole mount was calculated using epifluorescence microscopy, immunofluorescence staining and confocal microscopy. The total density of myeloid‐derived cells in the normal Cx3cr1^+/gfp cornea was 366 cells/mm². In BM chimeras 2 weeks post‐reconstitution, 24% of the myeloid‐derived cells had been replenished and were predominantly located in the anterior stroma. By 8 weeks post‐reconstitution 75% of the myeloid‐derived cells had been replaced and these cells were distributed uniformly throughout the stroma. All donor eGFP⁺ cells expressed low to moderate levels of CD45 and CD11b, with approximately 25% coexpressing major histocompatibility complex class II, a phenotype characteristic of previous descriptions of corneal stromal macrophages. In conclusion, 75% of the myeloid‐derived cells in the mouse corneal stroma are replenished after 8 weeks. These data provide a strong basis for functional investigations of the role of resident stromal macrophages versus non‐haematopoietic cells using BM chimeric mice in models of corneal inflammation.