Ekins then earned his HND Science Applied Biology from Nottingham Trent University (formerly Polytechnic, 1988–1991), graduating in 1991, with a sandwich year (1989–1990) at the pharmaceutical company Servier in Fulmer, UK where his interest in drug discovery was established.

Ekins then earned his MSc in Clinical Pharmacology (1991–1992) at the University of Aberdeen with a dissertation entitled "Speculations on the relative roles of cytochrome P450 and flavin containing monooxygenase in the metabolism of S12363"[1] he then earned a PhD in clinical pharmacology, at the University of Aberdeen in 1996, funded by Servier, and wrote a thesis entitled "Maintenance and cryopreservation of xenobiotic metabolism in precision-cut liver slices.

From 1996-1998 Ekins continued his research as a Postdoc at Eli Lilly and Company laboratories characterizing the little-known CYP2B6 and applied computational methods to this enzyme.

In 2004 he joined GeneGo (now owned by Thomson Reuters) as vice president, Computational Biology and developed the MetaDrug product (patent pending).

In 2015, Ekins founded Collaborations Pharmaceuticals, a privately owned company that performs research and development on innovative therapeutics for multiple rare and infectious diseases.

Ekins has also carried out independent research and collaborative research on topics including pharmacophores for drug transporters, cheminformatics for predicting immunoassay cross reactivity, models for studying nuclear receptor-ligand co-evolution, computational models for PXR agonists and antagonists as well as analyses of large datasets and crowdsourcing data.

How pharmaceutical companies could use open source molecular descriptors and algorithms which would facilitate computational model sharing with the academic and neglected disease community[25] This work is important because it was the first prominent advocacy for making a broad array of approaches to make preclinical and postmarketing data and models available as well as the demonstration of the feasibility of such approaches.

Ekins served on the advisory group for ChemSpider and provided an array of pharmaceutical data sets to the database to make it available to the community.

While working for Collaborative Drug Discovery, (funded by the Bill and Melinda Gates Foundation) he analyzed data provided to the public domain by the pharmaceutical industry.

[37] Using their respective blogs, Ekins and Antony Williams alerted the scientific community within days of the release of the NCGC NPC browser.

To date they have obtained 8 orphan drug designations across 5 rare or neglected diseases, and have widely published their results in peer reviewed journals.