Mrs Morgan, 50, is currently strategic services director at Sevenoaks DC where she has been since 1999.
South Northamptonshire Council leader Sandra Barnes said:
'Jean demonstrated a great deal of enthusiasm and energy during the two days that she was here for our selection process, as well as clearly being well informed about our district.'
Mrs Morgan hopes to take up her post by the beginning of August.
She replaces Robert Tinlin who moves to Southend-on-Sea BC as chief executive.