The front page of the weekly title states "Sunday Herald says Yes" and is decorated with a giant thistle and saltires in a design by artist and writer Alasdair Gray, who also supports independence.
An editorial article in the paper reads: ''Scotland is an ancient nation and a modern society. We understand the past, as best we can, and guess at the future. But history is as nothing to the lives of the children being born now, this morning, in the cities, towns and villages of this country.
"On their behalf, we assert a claim to a better, more decent, more just future in which a country's governments will be ruled always by the decisions of its citizens.''
The paper supported the SNP in the 2007 and 2011 Scottish Parliament elections. It said it will remain balanced in its reporting.
An article on the newspaper's website said: "The Herald & Times Group, publisher of the Sunday Herald, The Herald and the Evening Times, is giving the titles' editors freedom to take their own editorial position on the constitution. The company is non-political and neutral.
"The Herald has not declared an opinion on the referendum question. It will be up to its editor to decide when and if to do so."
The editorial in the Sunday Herald says it views the referendum as a choice between a "bankrupt, political structure" and the chance to "remake our society in a more equal, inclusive, open and just way."
The newspaper said it believes that a currency union is probable and is confident that Scotland will be a member of the European Union.
It also said that Scotland's media should reflect the diversity of opinion within the country and should not speak with one voice.
It said that this diversity of opinion is reflected within the Sunday Herald's own staff, with some supporting independence while others do not.
Some are still considering the arguments, it said.
Blair Jenkins, Yes Scotland chief executive, said: "The Sunday Herald is the first national newspaper to endorse either side in the debate about our country's future and we are delighted that it has chosen to support a Yes."
He added: "The Sunday Herald's editorial is passionate, inspiring and, above all, a statement of common sense and irresistible logic.
"It is also a very timely intervention following an analysis of the polls this weekend which confirm that support for Yes continues to build while backing for No is sliding backwards.
"What all of this tells us is that more and more people are reaching the conclusion that a Yes vote on September 18 is an opportunity too good to miss.
"With Scotland's future in Scotland's hands we can, should and must build the kind of country that we know Scotland can be."
SNP Westminster leader Angus Robertson said: "This is a very welcome decision by the Sunday Herald and is yet more evidence of the growing momentum behind the Yes campaign.
"The Sunday Herald's editorial gets to the heart of why Scotland can, should and must be independent - the chance to make Scotland a fairer, more progressive country.
"The UK is the fourth most unequal society in the developed world - and with Westminster's welfare cuts and further austerity measures the situation will only get worse.
"With the full powers of independence, we can choose to take a different path and get on with creating the better, fairer, more prosperous country described in the Sunday Herald's eloquent editorial."