In the 1999 general election, Fong won the Batu Gajah parliamentary seat in the Dewan Rakyat, and became the youngest female Member of Parliament (MP) in Malaysia. She won 19,867 out of 38,774 votes, winning by a majority of 2,071 with 67.5% turnout. During her first term, she was suspended for six months from Parliament without wages or allowances for criticising the Speaker of the House. Her suspension was unique in that the Speaker had waived the seven-day notice period required to raise the issue, and that the matter was never brought to the Parliamentary Committee of Privileges. The 83 MPs, all from the Speaker's party, who voted for suspension only constituted 43% of parliament; while this was a majority of those present in the hall, it did not have a simple majority of the total number of MPs. The suspension was widely seen to be vindictive.
In 2003, Fong inquired in parliament why she had been compelled to wear the tudung for her graduation ceremony at IIUM. The Parliamentary Secretary to the Ministry of Education, Mahadzir Mohammad Khir, stated wearing the tudung was encouraged but not mandatory. A year later, the IIUM Senate made it compulsory for female students to wear the tudung to their convocation ceremony.
In 2005, having noticed a few non-Muslim women wearing the tudung in the gallery, she raised a point of order about whether wearing the tudung was compulsory in Parliament. It was not.
Fong initially decided not to defend her seat in the 2008 general election. After DAP leaders asked her to reconsider, she finally agreed to run for re-election, retaining her Batu Gajah parliamentary seat for the third term with a majority of 24,627.
