A spectator was ejected from Exeter City's clash with Harrogate Town at St James' Park on Tuesday night.
It was the first time the Devonshire club had opted to take the knee before a home clash.
Recent incidents have again shone a light on racism and clubs have looked to underline their support for the Black Lives Matter movement.
But one fan at St James Park booed once the referee blew the whistle to signal players taking the knee.
He was drowned out by applause from around the ground and was subsequently thrown out of the IP Office Ltd Stand ten minutes into the contest.
A spokesman for Exeter City Football Club said: "We would like to thank the vast majority of supporters who supported our players when they took the knee as part of tonight's EFL wide campaign.
"Unfortunately one supporter was ejected from the stadium and the club will take the appropriate action."
It is the second time in three home Exeter games that a racist incident has overshadowed proceedings.
An allegation of racist abuse was made by a Northampton player last week and the club as well as the police have launched an investigation.
It follows recent high profile events at Millwall and PSG.
The London club's fans booed their players taking the knee upon their return to the Den.
They have since showed solidarity however when they held up a banner pushing for equality in their game against QPR at Loftus Road.
While in the Champions League clash in Paris the fourth official was criticised for an alleged racist remark directed at an Istanbul Basaksehir coach.
The Romanian official has since been banned but could quit the game alltogether.
