Wilson, 41, will spearhead the company's commercial offering, formulate and execute strategy and liaise with EAL's sister organisation Semta – which is engineering skills for the future.
She previously spent four years as EAL's product innovation manager.
Julia Chippendale, EAL managing director, said: "Natalie brings a wealth of experience and knowledge of the skills arena and sectors we operate in. She has a finely focussed vision of how we will evolve – and an extraordinary drive to deliver."
Wilson, a former apprentice, has previously worked nationally and internationally with Transco and British Gas. She was apprenticeship manager for ConstructionSkills before becoming a head of faculty at Rotherham College.
Leeds College of Building appointed Wilson work based learning manager to manage the provision for construction apprenticeships.
EAL is the specialist-awarding organisation for industry qualifications. In the last 10 years, 1.3 million people in the UK embarked on an EAL qualification.