Hanina earned his title due to the role he fulfilled - as Deputy to the Kohen Gadol (High priest) in the Holy Temple of Jerusalem. Ha-Segan was a position with the responsibility of overseeing the actions of the work of the Temple's priests (Kohens) staff, as well as a stand-in position, ready to take the role of High priest in case he will be found unfit to serve the holy work on the temple. In that conjunction, Hanina was considered a "Segan Ha-Kohanim", only second to the High priest, as R. Hanina himself indicates:
"R. Hanina the Segan of the priests said: Why a 'Segan' [Deputy] is ever appointed ? In case the high-priest became unfit for service, the 'Segan' [Deputy] should enter at once to do the service".;
At his time, many High priests reshuffled, while he remained in his role, and for that reason, it is believed to be the possible reason he was named 'Segan ha-Kohanim' rather than the more common term used in the Gemara: 'Ha-Segan'.