An indexing system for an in ovo injection apparatus is provided. Such an indexing system provides a positioning scheme for an egg carrier carrying a plurality of avian eggs to an injection assembly for injection thereof. The indexing system includes an initial stop provided to abut the trailing end of the egg carrier to form a first egg carrier position such that a first subset of the plurality of avian eggs is injected. An intermediate stop is provided to abut the trailing end of the egg carrier to form a second egg carrier position such that a second subset of the plurality of avian eggs is injected. An associated method is also provided.
