Zunika Ahmad, who has two wives and was diagnosed with gender dysphoria or "a strong desire to be male", pleaded guilty to committing an obscene act with the then 13-year-old girl.
Zunika had assumed "a role as a male to the extent of obtaining a fictitious identity and being married to females", a psychiatric report stated.
Her sexual disorder was discovered after her arrest and remand at Changi Women's Prison, Channel News Asia (CNA) reported.
Zunika's wives were also under the impression that they were married to an Indonesian man. The first wife became pregnant after having an affair, but told Zunika the baby was hers.
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She and the victim subsequently grew close and developed feelings for each other in 2012, according to the report.
Although the acts were committed with the girl's consent, they are still illegal as the age of consent in Singapore is 16 years, the report said.
The abuse came to light in March 2014, when the girl made a police report after an argument with Zunika.
Several medical reports produced in court today similarly concluded that while Zunika is biologically female, her psychological state is that of a male.
Doctors also did not find that Zunika required any psychiatric treatment. The only treatment necessary is sex reassignment surgery, her lawyer N Sudha Nair said.
Nair told the court that Zunika intends to undergo surgery after serving her sentence, and continue living with her wives and daughter, who have come to terms with her "disorder of sexual identity".
However, he urged the court to impose a sentence of eight years' jail based on relatively similar cases.
Citing the complicated and unprecedented nature of the case, Justice Kan Ting Chiu said he would issue the sentence at a later date. Fourteen other similar charges will be taken into consideration during the sentencing.