The announcement comes as its focus shifts to the 2026 Holyrood election.
The SNP, which has been in power since 2007, faces a resurgent Labour Party which increased its Scottish seats at Westminster from one to 37 in the summer’s general election.
Mr Kerr said: “The national executive committee has been tasked with delivering a modern, dynamic election-winning party to win in 2026 and beyond – and today’s agreement to consult on a new structure at headquarters makes key progress to deliver on that aim.
“The proposal, agreed by the SNP National Executive Committee today, would get HQ into shape for future elections and for the fight for independence.
“It would mean that not everyone currently employed at HQ will continue with us but a streamlined headquarters protects the long-term finances of the party and delivers on the modern, professional, election-winning organisation Scotland needs.”
Mr Kerr said the SNP’s success was built on the work of many people – at headquarters, in local campaign teams and those in elected office.
He also thanked those who worked for the party and supported its aim of an independent Scotland.