Rebecca Welch, 37, will be in charge for Monday's League Two match between Harrogate and Port Vale.
Welch, the Football Association's highest ranking female referee, has officiated a number of high profile women's games including the 2017 FA Cup final and internationals.
"It was a shock," said Welsh, who is from Washington, Tyne and Wear.
"I got a phone call from [referees chief] Mike Jones and my initial response was - 'Oh what've I done?!'
"But I'm really excited and this is what I've been working towards. Being given this opportunity to work in the EFL is amazing for me."
In 2010, Amy Fearn refereed the final 20 minutes of Coventry against Nottingham Forest following an injury to the match official, but Welch is the first woman to be appointed to a game.
Welch is one of several officials working in the men's game, having already been added to Uefa's elite women's list along with Sian Massey-Ellis in the Premier League, France's Stephanie Frappart and Germany's Bibliana Steinhaus.
"I was just given the appointment and I was over the moon but when you kind of reflect on it you think you're the first woman ever to do this, so I'm extremely proud and my family's extremely proud as well," Welch added.
"I do think it's important to show that women who are in the top 1% of their category can proceed to the next level so it definitely makes others down the period look up and know that they can achieve the same.
"It shows that there is a real opportunity for young girls who are wondering if they are to take the whistle or who are already referees, that they can aspire to be an EFL referee or like Sian Massey-Ellis operating in the Premier League.
"In the last 10 years I've put a lot of hard work and commitment in and I've reaped the rewards from that by getting promoted.
"But I'd never seen myself as a trailblazer until the last year where I've started to accept it because I think it's important that people who are fortunate enough to be in my position or similar can show people that this can be done."