He has taken over at the Midland League Premier Division outfit, which finished 15th last season.
Funk, who has also had a successful spell at Scarborough Athletic as well as at the Wrens and the Bulls, guided AFC mansfield into the Evo-Stik Northern Premier League before leaving earlier this year.
Long Eaton managing director Nick Dargan said: “We are delighted Rudy has agreed to join us. Anyone who knows or has met him cannot fail to be impressed by his knowledge of non-league football, his enthusiasm for the game and his proven track record.”
Funk has taken over from former Mansfield Town manager Paul Holland and Andy Todd, but Dargan said both would remain at Long Eaton.
“Dutch (Holland) and Andy Todd have done an excellent job in the second half of the season,” he said. “It has become obvious though that the club needs Dutch to continue his work developing our highly-talented young CFC and Academy sides, whilst Toddy will be offered a role in the new set-up.”
Funk added: “I have been offered a number of great opportunities but have met chairman Jim Fairley and the Long Eaton United Board and discussed their vision for the club and seen first-hand the impressive plans for the development of the facilities here,”