Previously, Flynn acted as caretaker manager alongside the club's skipper Rob Jones who is set to become player-coach as part of the new lineup.
The Rovers were expected to finalise a shortlist of candidates today after looking through applications on Tuesday.
However, Flynn and Jones were clear favourites during Tuesday’s discussions and were offered the job at lunchtime today.
More top news
Emma Jesson brings you Sunday evening's forecast for Yorkshire and Lincolnshire
Wet and windy spells, interspersed with drier interludes this week. Wintry showers and variable temperatures. Gales and a weather warning
Mainly dry and cloudy today, rain on and off, some bright spells. Milder than of late but breezier