Clark, who was fired by the League One club last week, presided over the longest unbeaten run in the side's history, seeing them go 43 regular season league matches without a loss to set a new Football League record.
The 39-year-old former Newcastle, Sunderland and Fulham player took over as Huddersfield manager in December 2008 and left with the Terriers fourth in the League One table.
However, Clark's achievements were not deemed to be enough for Huddersfield chairman Dean Hoyle, who defended his decision to sack him earlier this week by saying he had lost faith in his ability to secure automatic promotion.
Despite this, Clark - who has now been replaced by former Leeds boss Simon Grayson - has been shortlisted alongside Brighton manager Gus Poyet and Crystal Palace boss Dougie Freedman for the award, which is voted for by Football Manager website users.
In a statement, the Football League supported Clark's inclusion on the shortlist following his success during 2011.
It said: "The Outstanding Managerial Achievement Award recognises exceptional individual achievement over the last calendar year.
"Lee Clark led Huddersfield Town to a run of 43 unbeaten consecutive League games during this period - a new Football League record.
"For this reason he was voted for by fans, before he left Huddersfield, as a fitting candidate for this award."
The Football League Awards 2012 will be held in London on March 11.
Clark, meanwhile, insists speculation linking him with other clubs had nothing to do with his sacking.
Although he had to distance himself from rumours linking him with positions at Leicester and Leeds in the past, Clark feels that should not have influenced Hoyle's decision to sack him.
"I wouldn't like to think so. Surely it's a compliment," he told TalkSport.
"All these clubs that came in for striker Jordan Rhodes. Does that mean because they are linked to our outstanding players, we are going to move them on because we get disappointed by them getting linked?
"It's the same with the manager. If I was doing a poor job, nobody would have been interested in me."
Clark expressed his shock at the decision to end his tenure at Huddersfield and has urged Hoyle to carry out his dismissal in the correct manner.
"I would just like it sorted out in the right and proper manner. I worked extremely hard for the football club," he said.
"I have moved it forward huge strides and we always talked about our relationship, myself and the owner.
"There is not just me, there are three other great lads there. Terry McDermott, Paul Stephenson and Steve Watson have themselves and their families to consider.
"Huddersfield have moved on with their new management team, they just need to do it the right and proper way so we can move on with our careers."
Despite his exit, Clark has revealed he wished Hoyle and his successor Grayson, all the best for the future.
"I've got nothing but great things to say about that football club. I had a great relationship with the owner and that's why I dont want it to end the way it has, in terms of some things that have been said," he said.
"I texted him to say he has made a good appointment and I hope they go for promotion.
"I have spoken to Simon since through a text and they are unbelievably positive because they know the quality of the squad and the group, the whole set-up and the whole infrastructure."
