Ian Price, 40, replaces Colin Smyth, who stepped down last year after 10 years working for the party.
Mr Price is currently the head of public affairs and marketing at RSPB Scotland, where he has spent six years.
A member of the party for more than 20 years, he has previously worked for Labour as an organiser in the North East of Scotland.
Leader Johann Lamont said: "We all look forward to working with Ian as we continue to change our party.
"The rebuilding process is already under way and Ian's experience will be invaluable as Scottish Labour prepares for a crucial period in our - and Scotland's future - with a referendum and elections for Europe, Westminster and Holyrood in the next three years.
"Ian's appointment as Scottish Labour's most senior official is an important step towards making our party once again where people turn to help meet their hopes and aspirations."
Mr Price said it is an "exciting time" to be involved in Scottish politics.
"I look forward to helping Scottish Labour achieve our goals." he said.
"I believe Scottish Labour will have a key role in deciding the future of our country, both through the referendum and in the coming elections, and I want to play my part by helping Johann Lamont and the Labour team deliver for Scotland.
"I share Johann's appetite to modernise the party, change the way we engage with people of Scotland and offer them an exciting vision of what Scottish Labour believes Scotland in the 21st century can be."
An SNP spokesman said: "Congratulations to Ian Price on his appointment. Given that the latest opinion poll in Scotland puts the SNP at the same 45% record level of support that delivered our landslide re-election in 2011, Mr Price clearly has his work cut out."