The MP for Peterborough, who could be removed from her role in seven weeks, was joined by fellow city MP Shailesh Vara, the Conservative member for North West Cambridgeshire, in siding against Prime Minister Theresa May’s Withdrawal Agreement which was defeated by 391 votes to 242 votes - a majority of 149.
With Brexit Day of March 29 fast approaching, MPs will now vote tomorrow on whether to rule out leaving the EU without a deal. If this is successful MPs will then vote on Thursday on whether to ask for an extension of Article 50.
Ms Onasanya had not previously voted in the House of Commons since January 28.
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She was convicted in December at the Old Bailey for perverting the course of justice and sentenced in February to three months in prison, of which she served four weeks.
Her vote tonight could be one of her final acts in the Commons as a Recall Petition to remove her as MP opens on Tuesday.
The petition was automatically launched after Ms Onasanya failed to overturn her conviction for lying about who was driving her car when it was caught speeding in Thorney in July 2017.
If 10 per cent of her constituents (around 7,000 people) sign the petition within a six week period then she will lose her seat and a by-election will be triggered.
The MP was expelled by the Labour the day after her conviction and is currently sitting as an independent.
She has previously voted against the Government’s Brexit deal when it was first put before MPs in January, but has missed several other important Brexit votes without giving a reason.
Mr Vara also voted against the Withdrawal Agreement at the first meaningful vote before it was sent back to Brussels to try and secure legally binding changes to the Northern Ireland backstop.
However, Attorney General Geoffrey Cox admitted today the legal risk of the UK being stuck in the contentious backstop remained.
How other MPs voted
Steve Barclay (North East Cambridgeshire) - For the deal
Nick Boles (Grantham & Stamford) - For
Jonathan Djanogly (Huntingdon) - For
John Hayes (South Holland and The Deepings) - For
Tom Pursglove (East Northamptonshire) - Against