The campaign will stress the importance of vaccination and try to improve take-up of the vaccine. A DH survey suggests few pregnant women are aware of the outbreak.
The HPA has reported 4,791 cases of pertussis so far in 2012, four times the total for 2011.
Advertisements and features in women's and pregnancy magazines and online will run from the end of October until February, with a break for Christmas.
In a letter to the NHS, England's CMO Dame Sally Davies said there was 'little awareness of the current outbreak' or the potential severity of pertussis in neonates among pregnant women.
RCGP immunisation spokesman Dr George Kassianos said he was 'very pleased' a campaign would be launched. 'The health and survival of the neonates is too serious a problem and it cannot be left to chance that GPs will do a good job. The DH needs to help GPs do a superb job, hence the need for this campaign.'
No flu campaign
However, Dr Kassianos questioned why the DH will not run a similar campaign for flu vaccination in pregnant women and other at risk groups. Last winter, just 25.5% of health pregnant women chose to have the jab.
He said: 'I cannot understand why we do not have a national campaign for flu immunisation. If we take influenza seriously in the UK then a national campaign is of paramount importance if we are to achieve excellent immunisation rates among the vulnerable.'
A DH spokesman said: 'Local NHS organisations across the country are running their own flu campaigns to raise awareness of the vaccine.'