Ms Sturgeon has swapped roles in the Scottish government with Alex Neil, who moves to health from his previous role as infrastructure, investment and cities secretary.
Ms Sturgeon, also Scotland’s deputy first minister, will now take the lead on an independence referendum.
Dr Brian Keighley, chairman of BMA Scotland said: 'Mr Neil comes into the NHS at a difficult and interesting time. There are escalating challenges for the Scottish NHS as it struggles to cope with growing financial pressures, which will have an adverse impact on many patient services and create additional pressures on the already hard-pressed NHS workforce.
'The thorny issue of changes to the NHS pension scheme in Scotland also remains to be resolved. We look forward to working with Mr Neil to respond to these challenges.'