The Department of Health is thought to have seen presentations from five agencies outlining online strategies before making the appointment.
The campaign will run early in 2007 to coincide with the traditional wave of New Year's resolutions among smokers planning to give up.
It comes ahead of a ban on smoking in workplaces across England and Wales.
Profero is creating the Smokefree England website, which will carry information on the ban, while Farm will develop a £10 million ad campaign to offer advice to smokers.
The agency shares the COI anti-smoking advertising account with Miles Calcraft Briginshaw Duffy.