His adoptive parents, lesbian couple Pauline Moreno and Debra Lobel, have defended the decision for Thomas, who now calls himself Tammy, to begin treatment to change sex at such a young age.
They believe children with gender identity disorder - or gender dysphoria - who are forced to propose transitioning into adulthood face a higher risk of suicide. Last week we covered the story of 10-year-old Livvy James who left school as a boy and returned to school after the summer holidays as a girl with her parents' blessing after being diagnosed with gender dysphoria.
The couple from Berkeley, California, are adamant they have not pressurised him into making the decision to become a girl; that one of the first things Thomas told them when he learned sign language aged three, learned because of a speech impediment, was, 'I am a girl'. Pauline says Tammy was shy and unhappy as a boy compared to his older, more outgoing brothers.
At age seven, after threatening genital mutilation on himself, psychiatrists diagnosed Thomas with gender identity disorder. By age eight, he began transitioning.
This summer, he started taking hormone-blocking drugs, which will stop him from experiencing puberty.
The hormone-suppressant, implanted in his upper left arm and replaced every year, will postpone the 11-year-old developing broad shoulders, deep voice and facial hair, by blocking his hormones.
But Pauline and Debra faced criticism from friends and family - although they are now supportive. Pauline said: 'Everybody was angry with us. "How could you be doing this? You might be ruining his whole life!"
Citing a statistic from the Youth Suicide Prevention Program, Ms Moreno noted over 50 per cent of transgender youth will have had at least one suicide attempt by their 20th birthday. She hopes her son's sex change will help him have a happy adulthood.
'What is so frightening to me is that you would be willing to say "no" just because you don't like it - even though your child could lose their life?'
Pauline said: 'The whole idea now is let's stop creating a third (gender) that is neither one thing or the other, so we transitioned her.
'The protocol now is to transition these children as soon as you can make a diagnosis, because otherwise they end up being not one thing or the other... because they experienced puberty.'
Pauline explained: 'She will stay as a pre-pubescent boy until she decides and we feel that she can make this decision about surgery.'
His parents say the hormone treatment will give him time to figure out if he wants to fully transition to being female or go through puberty as a boy.
By age 15 the device will need to be removed. If he chooses to stop taking the drugs, he will undergo natural male puberty at a later stage and his future fertility would not be impacted.
Should their son decide to transition to an adult female, he can take female hormones as well, which would raise his voice, allow him to grow breasts and develop other feminine physical characteristics.
The first steps of Thomas's transition was allowing him to pick his own clothes - and he went straight for dresses and hair bands.
Pauline says the change in his personality was immediate: 'He was in his own world just completely detached and that was a problem we always had was getting Thomas to participate in life,' she said. 'What we saw emerge when Tammy was allowed to be Tammy is, "Whoa!"... It was an immediate transformation. She was so giggly and she was now interacting she was now making it a point to defend herself.'
Tammy's parents say the diagnosis has been hard for them to accept - but that they want to do the best thing for Tammy, who they adopted aged two.
The couple were married in 1990, and had a commitment ceremony with a rabbi in synagogue, and have two older sons and grandchildren.
'It was odd to us,' she said. 'Even though she has lesbians as parents, this is all new to us in every possible way. We know what it's like to feel different - we've got that one. But to feel like you're not in the right body was just something we could not put our heads around.'
Fortunately, the family has a vast support system. The couple credits Tammy's teachers and officials at Children's Learning Center in Alameda, California, and their religious community, for being open-minded about their son's decision.
'We live in the Bay area where lots of alternative lifestyles are in place... and we belong to a religious community that was incredibly supportive. They make it a point when we're in synagogue to come over and tell Tammy, "Oh, you look so pretty today,' Ms Moreno said, adding, 'There's never going to be enough gratitude for them.'
San Francisco, next to Berkeley, is one of four cities in the United States with a hospital that has a specific programme for transgender children, offering long-term counselling with mental health professionals and treatment by paediatric endocrinologists.