Hertfordshire County Council says Tala the Storyteller is a "bright, vibrant creature" and will be referred to using they/them pronouns.
Tala will take over from Bookstart Bear at children's reading events across the county's 46 libraries.
As Bookstart Bear is withdrawn nationally, Tala will be the new mascot for a series aimed at babies and toddlers.
A picture of the alien can be seen on personalised library cards for under five-year-olds.
Tala the alien
Hertfordshire County Council
A library card featuring Tala the alien
Hertfordshire County Council
The character is meant to "inspire families with babies and young children to visit the library regularly," according to a council spokesperson.
Maya Forstater, a high-profile campaigner on gender, took issue with the alien and claimed it was "trans".
She tweeted: "A mother with her baby daughter at Hitchin Library Rhyme time aimed at 0-five-year-olds messaged me.
"Bookstart Bear has been retired and replaced with Tala, a 'trans' bear, with they/them pronouns.
"I cannot express how upset I feel. Why do children need this?"
In another tweet, she wrote: "Why is Herts County Council promoting gender ideology to under 5s? This is indoctrination in a belief system."
But libraries were quick to hit back, with Hitchin Library writing: "Just to confirm – Tala isn't trans, they are an alien."
It added: "Tala is a storytelling alien from outer space, so neither male or female."
A spokesperson for Hertfordshire County Council said: "Tala is not 'trans' and any suggestion that the character is would be grossly misleading and wildly inaccurate.
"Tala is a fictional character, which is clearly based on an other-worldly creature to capture the imagination of children and young people using Hertfordshire's libraries.
"In the absence of a gender for this alien creature, we simply use gender-neutral language when talking about them to the public."
