Independence supporters marched through Glasgow on Saturday.
The Aberdeen South MP said Scotland’s problems would not be fixed by Mr Johnson’s resignation and only Scottish independence would be the way forward.
“As you know, as I know, as everyone up and down Scotland knows, this Prime Minister is a charlatan, this Prime Minister is corrupt and this Prime Minister is a liar,” he said.
“The reality is, over the course of the last year or two, what we’ve seen is a Prime Minister who’s just taken £20 away from the poorest in society when we’re on the brink of a cost-of-living crisis.”
He added: “This is a man who partied … whilst people across Scotland and across the UK were dying.
“Boris Johnson needs to go and he needs to go now.”
Issues in Scotland with the UK Government “don’t start and they don’t stop with Boris Johnson”, Mr Flynn said as he touted the need for the country to leave the union.
“Not since 1955 – some 70 years – have the people of Scotland endorsed the Tories at the ballot box, yet we have been the ones who have had to bear the brunt of their policies.
“Their policies hammer the poorest in society while they feather their own corporate nests, while they continue repeatedly to ignore the democratic views of the people of Scotland.
“So, Boris Johnson, doesn’t just need to go – the Tories need to go too.”
The SNP business spokesman at Westminster went on to describe the UK Parliament as “an antique” which “doesn’t care about you or me or anyone else up and down Scotland”.
He continued: “Let’s be done with Boris Johnson, let’s be done with the Tories, let’s be done with Westminster and let’s be done with their union.
“Let’s build something better, let’s build something that’s got compassion at its heart, that’s got people at its heart, that’s got our values and our principles at its heart.”
Alba Party MP Neale Hanvey also addressed the march, calling on the Scottish Government to call a constitutional convention “to chart our path to independence”.