Funk took over the Cobras in late November, replacing Dave Hoole, but has overseen only two victories in that time and his team having not scored in their last four matches.
Clipstone sit 19th in NCEL Division One, three points from safety and having played a game more than the clubs immediately above them.
The Romanian-born Funk has managed at many clubs in the local area but has been unable to reverse the Cobras’ fortunes as they battle to avoid dropping to step seven of the pyramid.
They are now set to appoint an interim boss to see out the remainder of the season which sees Clipstone only having five games left to play.
The club’s vice-chairman Paul Griffiths said: “There is still a lot to play for in the final five games we have left this season, and although the short term pathway ahead is uncertain, we still have some major plans for the club longer term and we’re sure we will find the right management team to take us there.
"We are looking to build the foundations of the future Clipstone FC and the community for decades to come.
"The lads all seem geared up to give their all for the cause, and we can’t ask any more than that from them.
“We would like to wish Rudy all the best for the future in what ever he does. We will now re-group and look to finish the season with an in-house interim management team.