Videos, including some members of the community discussing their lives, were taken down and others complained of having the sound removed.
TikTok defended its actions, stating that some posts were deleted for breaking guidelines on smoking and nudity, but could not explain why others were removed.
‘Sending a negative message to young transgender people’
LGBT charity Stonewall said this action by the social media giant sent a negative message to young transgender people who use the platform to express themselves.
In a statement, the short form video platform said, “TikTok is an inclusive space for positive and creative expression. We categorically do not remove any content on the basis of expression of gender identity.
“We have a vibrant and diverse community on TikTok: there are nearly two billion views of content under #trans and over 2.1 billion views of content under #lgbtq.
“We are proud to be a platform for positive and creative expression for our diverse community of users.”
Reice Hodges, 35, told the BBC she had several videos removed, including one where she challenged instances of bullying. She claims TikTok deleted these posts before removing the abusive comments she received.
“It makes me mad when my content is removed. There are some videos that I spend hours making… and to have one of those videos removed really discourages me,” said Hodges.
“There are countless amounts of teenagers and adults who have reached out to me and thanked me for putting myself out there to be seen.
“To block something that can bring awareness to the trans community, when we already have so much hate and disgust coming toward us – where else are we supposed to go?”
Other users complained that their videos showing their transition in photographs were removed, although they were later able to repost them.
This is the latest in a series of controversies to affect TikTok in recent months. In December, the app’s moderators acknowledged videos made by disabled users were prevented from going viral, due to a policy it said was designed to reduce the amount of cyber bullying on its platform.