A report by Health Protection Scotland said that while diagnoses of pertussis had fallen in 2014, the level remained above average.
The HPS weekly report said: "In 2012 and 2013 Scotland, like the rest of the UK, experienced an outbreak of pertussis with a total 1927 and 1188 laboratory-confirmed cases in 2012 and 2013 respectively.
"While the weekly incidence has now declined compared to the same time in 2013, with 98 laboratory-confirmed cases in the first 12 weeks of 2014, compared to 479 during the same period in 2013, the level of pertussis still remains above the levels historically seen in Scotland over the previous 10-year period."
In 2010 there were 82 confirmed cases, and 119 in 2011.
Infants are the group most likely to develop complications from whooping cough, which in severe cases can be fatal.
A vaccination programme was introduced in October 2012 to protect pregnant women.