Since 2019, Rafaelita has served as Undersecretary of the Department of Trade and Industry- Competitiveness and Innovation Group (DTI-CIG). Prior to her DTI appointment, she worked as Senior Research Fellow and Vice-President of the Philippine Institute for Development Studies.

A researcher turned policymaker, she was highly instrumental in crafting the analytical framework for the Industry Roadmap Project and the formulation and implementation of the Comprehensive National Industrial Strategy, Inclusive Innovation Industrial strategy or i3S, and the new industrial policy known as the Science-,Technology-, and innovation- based Industrial Strategy or mindfacturing strategy. She has also led DTI’s innovation and Industry 4.0 initiatives such as Inclusive Filipinnovation and Entrepreneurship Roadmap, Smart Industry Readiness Index Assessment, Industry 4.0 Pilot Factory, Regional Inclusive Innovation Centers, Artificial Intelligence Roadmap along with Strategic Investment Priority Plan, Philippine Skills Framework, Creative Industry Development Program and the more recent Tatak Pinoy Industrial Policy Program.