In order to increase water productivity at the Collective Irrigation System (CIS) level it is crucial to adapt the existing irrigation infrastructure, enhancing water intake at the source, as well as its transport and delivery efficiency. Rehabilitation may involve structural changes and thus, a large capital investment. This investment should be proportionate to the increase in climate resilience associated to different rehabilitation alternatives. A methodology framework was developed to evaluate CIS resilience to climate change considering different rehabilitation alternatives. The assessed components were: (i) crop production systems; (ii) on-farm irrigation systems; and (iii) project rehabilitation alternatives for the conveyance and distribution of the irrigation water from the source to the farmer fields. This framework was applied to the Maiorga CIS, in central Portugal, to test the methodology performance in assessing the impacts of climate change on the supply-demand balance of the proposed rehabilitation alternatives and to evaluate their climate resilience, for the representative concentration pathways, RCP4.5 and RCP8.5, and two time periods, 2041–2070 and 2071–2100. For each scenario, period, and rehabilitation alternative, irrigation requirements at the source (demand) and stream flows (supply) were computed and the supply-demand balance was performed. Projected increases in irrigation water demand varied between 5.5% for RCP4.5/2071–2100 and 35.7% for RCP8.5/2071–2100. For RCP4.5, 11% (2050) and 9% (2080) reductions in irrigation water supply were projected, while for RCP8.5 the reduction ranges between 13% (2050) and 30% (2080). The proposed framework determined that the rehabilitation alternatives considering just one type of water source, without flow regularization and with open channel distribution to the farmer’s field, have proved to be unviable due to low resilience to climate change.