Union officials representing thousands of striking medical workers have signed an agreement with government officials in the capital, Nairobi.
The doctors are to receive increased allowances as negotiations over other issues continue.
The doctors have been demanding higher wages and better working conditions and say more doctors need to be hired.
About 2,500 public health institutions were affected by the strike.
A number of patients are reported to have died from a lack of medical care during the walkout.
"We are grateful that this dark page in the history of our country has come to an end," Health Minister Cleopa Mailu said at the signing of the deal.
The authorities would do their best to ensure Kenyans "get services quickly", he added, without giving exact dates on when public health services would be back up and running.
Dr Ouma Oluga, head of the union of medical workers (KPMDU), said: "The strike may be over but the industrial dispute is not yet".
He reiterated the union's argument that it was impossible to separate the rights of patients from the rights of doctors.
The return to work agreement will see doctors receive an additional $560 (Â£460) to $700 a month in allowances.
However a separate agreement, called the Collective Bargaining Agreement (CBA) is yet to be discussed.
The CBA could take weeks to conclude as the organisations that actually employ the majority of the doctors - the County Boards of Health - were not involved in drafting the document and they need to study it before the county governors can sign.
Previous attempts to end the strike failed as doctors and the government refused to compromise on their positions.
Last week the government withdrew its offer of a 50% pay rise to the workers.
The jailing of KPMDU union leaders for refusing to honour a court order to call off the strike failed to persuade the doctors to back down.
As well as higher salaries, doctors have been campaigning for improvements to dilapidated public health facilities and want Kenya to address a huge shortage of doctors.
Doctors in Kenya have agreed to end a 100-day strike that has paralysed the country's public health system.