A transport refrigeration unit (TRU) battery charging system includes a programmable transport refrigeration system (TRS) Controller, a TRU battery and a programmable battery charger (BC) programmed to transfer electrical current to the TRU battery via a predetermined current path through the programmable TRS Controller in response to a value of offset current drawn from the TRU battery by the programmable TRS Controller and subsequently communicated to the programmable BC by the programmable TRS Controller. The programmable TRU battery charger allows for a dynamic load characterization of the programmable TRS Controller and accessory loads based on programmable TRU battery charger internal shunt current measurements and programmable TRS Controller internal shunt current measurements to allow the programmable TRU battery charger to function properly with all intended modes of operation.