The Crusaders currently sit just two points outside of the play-offs, despite being tipped by many as relegation favourites following their promotion from the Evo-Stik Southern Premier League last season.
Their performance has kept up Wilkinson's record of securing seven consecutive top seven finishes during his time with the club.
However any thoughts of another promotion seem to have been dashed by the Football Association.
The Crusaders' Bulpit Lane home falls just one hundred seats short of ground-grading criteria to allow the club to compete in the National League play-offs.
The deadline for criteria has been passed, with the club confirming in a statement that they would appeal the FA's decision.
That appeal, along with those of Darlington and Poole Town, look set to go into the FA on Thursday.
Any hearing date is yet to be confirmed, leaving Wilkinson and his players in limbo as they go into the final two fixtures of the season against Wealdstone and Chelmsford City.
Wilkinson only found out about the decision an hour before the Crusaders' crucial 2-0 home win over fellow play-off challengers Dartford on Good Friday.
Now, with the play-off position under serious threat, Wilkinson admitted that he has sympathy for everyone at the club.
"I'm gutted, we are all gutted here" he said.
“It feels like maybe, as a club, we could have have missed an opportunity.
“I always believed in my players and myself that we could reach the play-offs and continue this wonderful success story we have at Hungerford Town.
“We keep surpassing expectations and keep setting new goals for ourselves and I have to say I always thought we could make the play-offs.
“People laughed and thought I was overly-confident but I know my squad.
“To be honest it is the players and the supporters I feel sorry for because the effort they have put in, not just over the season, but over the last three to four years, deserves a chance to play at the highest level”
Any promotion would allow the Crusaders to compete at the highest level in the history.
And it would allow Wilkinson, who has been linked with the likes of Maidenhead United and Eastleigh, to test his managerial skills against the best that non-league football has to offer.
Never one to hide his ambitious side, the former Reading academy coach revealed that competing in the National League would be a dream for not only himself, but for his players as well.
“We would all be disappointed (if the appeal was unsuccessful), that is obvious isn’t it?
“As a manager, just like my players, I want to test myself against the best managers and teams around.
“If we could do that in the National League, against some really big name clubs and managers, that would be a dream, not just for myself, but for the players.
“The thought of going up against former Football League clubs in the National League and above is what I thrive on.
“I am ambitious and I hope I can get that chance”
The thought of National League football is all a far cry from the club's time in the Hellenic League.
Their league title win in 2009 sparked a remarkable upturn in the club's fortunes, with last season's Southern Premier League play-off final win over Leamington elevating them into step two of the non-league pyramid for the first time in their history.
That has only added further fuel to Wilkinson's ambitions to continue both his own progress and that of the club.
“I have been at Hungerford Town for a long time now and I love the club.
“I enjoy working here and I enjoy working with my players, we have progressed so much together.
“That bond is what has made us successful during my time and I would love to take them higher in the pyramid”
Interview: Mark Carruthers (@marknldaily)
Image: Hungerford Town FC