Presiding officer Ken Macintosh said the flag will come down at 11pm on January 31, when the UK leaves the EU.
Boris Johnson has denied Nicola Sturgeon's request for indyref2 - but the battle doesn't end there.
The European Union (Withdrawal Agreement) Bill was passed by 330 votes to 231.
Constitutional relations secretary Mike Russell will take part in talks with UK Government ministers and counterparts from the Welsh administration.
MSPs voted to reject the UK Bill by votes to 92 votes to 29.
MSPs are set to debate whether to give consent to the agreement struck by Prime Minister Boris Johnson with the EU.
The SNP is on course to win a landslide of Scottish seats on December 12, our poll found.