He obtained his PhD (1992) from the Autonomous University of Madrid. He has been Postdoctoral Researcher at the University of Illinois (USA), Assistant Professor at the University of Oviedo, and Permanent Researcher at the ICMAB-CSIC in Barcelona. In 2007 he moved to the Catalan Institute of Nanoscience and Nanotechnology (ICN2), of which he has been director since 2012. He has published more than 220 scientific articles, with more than 35,000 citations.

His research interest focuses on the simulation of the properties of materials at the atomic level, using methods based on quantum mechanics. He is known for developing efficient numerical methods for very large scale simulations, with a reduced scaling with the size (number of atoms) of the systems being studied. He is one of the main co-developers of SIESTA, an open source DFT code for the study of complex materials, used by hundreds of groups worldwide.

Ordejón has been head of the Condensed Matter Physics area of ​​the Spanish Agency of Scientific Evaluation (ANEP) and of the Physics and Engineering Panel of the Spanish Supercomputing Network, and coordinator of the Physics area of ​​the Gadea Foundation. He is a Fellow of the American Physical Society and a member of the Academia Europaea, and received the Narcis Monturiol medal from the Government of Catalonia. He is currently a Trustee of the Barcelona Institute of Science and Technology (BIST). He was co-founder of SIMUNE Atomistics SL, a spin-off company that provides materials simulation services to industrial clients.