Phelan replaces Marc Astley, who announced his resignation in December.
Both titles were switched by Northcliffe in 2011 from a daily to weekly publication, the Herald Express in July and the Express & Echo in August.
Andrew Blair, managing director of Northcliffe's South West Media Group said: "I am delighted to welcome such a high calibre journalist and experienced editor to the Exeter business.
"The Express & Echo, as Exeter’s leading medium, operates in a vibrant growing city which rightly demands a lot from its local paper. I very much look forward to Andy being able to add a powerful new dimension to our business here."
Jim Parker, deputy editor of the Torquay Herald Express, will take charge of the title until a successor is appointed.
Several Northcliffe titles were switched from daily to weekly publication last year, with the Scunthorpe Telegraph and Lincolnshire Echo also making the move.
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