Rebecca Welch, 37, oversaw Port Vale's 2-0 win at Harrogate Town in League Two on Monday.
Ms Welch, from Washington, County Durham, has officiated seven National League games this season.
She is in the elite category of referees and is on FIFA's international list, Sky Sports said.
Amy Fearn was the first woman to referee an EFL game as she came on as an injury replacement in the 2010 Championship game between Coventry and Nottingham Forest.
But Welch was the first to be given a game from the off and had a day without any major controversy, barring a contentious decision to wave away Harrogate's appeals for a first-half penalty.
Harrogate manager Simon Weaver said he was impressed by Welch's performance and hopes her display signals the start of more women officiating in the EFL.
Weaver said: "I think she was very good indeed. Important calls were made throughout and they were the right calls.
"Hopefully it's just par for the course that we see female referees and officials in the EFL. It's about time."
Port Vale boss Darrell Clarke agreed with his opposite number's assessment of Welch.
"I thought she was focused and didn't get much wrong. I was moaning about one or two decisions, but generally it was quite consistent.
"We need to see more women referees and lineswomen moving forward. They should be judged like anyone else and she's had a good start."
Speaking after her appointment was announced last week, Welch told the EFL's official website: "Initially I wasn't really aware of being appointed as the first female referee.
"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."
Monday's game took place without fans due to coronavirus restrictions.
According to the government's roadmap out of lockdown, up to 10,000 fans could attend outdoor sports matches from 17 May.