He was nominated for the post by ministers last month but the appointment had to be approved by the House of Commons environment, food and rural affairs committee. This approval has now been given.
Sir Philip will take up the £100,000-a-year post in September, when the term in office ends of Lord Smith of Finsbury, the former culture secretary.
The committee questioned the civil engineer about his previous experience and suitability for the role, considering his business skills, dealings with government and media-facing experience.
Sir Philip Dilley is expected to spend two or three days a week on the job, which employs around 10,600 staff and is the frontline service for flood protection, environmental regulation and water resource management.
Committee chair Anne McIntosh said: “We are satisfied that Philip Dilley has the professional competence and personal independence required for the post of chair of the Environment Agency. We wish Mr Dilley every success in his new post.”