Montserrat Serra and Blanca Thiebaut, 40 and 30 respectively at the time of their kidnapping from the Dadaab refugee complex near the border with Somalia in October 2011, are both "safe and healthy", MSF said.
"Both are safe and healthy and keen to join their loved ones as soon as possible," the medical charity said, without disclosing when they were released or how.
MSF said it would give no further details before a press conference scheduled in Madrid on Friday.
Serra and Thiebaut, both logisticians, were seized by armed men in the Ifo camp in Dadaab, where they were working on the construction of a hospital, and immediately driven across the border.
Kenyan police said they had been taken by members of Somalia's Islamist Shebab group, but no group has actually claimed the kidnapping.
MSF, which at the time of the kidnapping had 49 foreign and 343 local staff in Dadaab, reduced its activity there to a minimum.
The abduction of the Spaniards followed the kidnapping of a French woman and a British woman from the Kenyan coast near the Somali border.
Briton Judith Tebbutt, in her late fifties, was seized from a remote Kenyan resort on September 11, 2011 by armed men who killed her husband David. She was released in March 2012 after being held for more than six months, reportedly after her son paid a ransom.
Marie Dedieu, 66 and partially paralysed, was seized from her beachfront home in the Lamu archipelago on October 1, 2011.
Just days after the two Spaniards were seized Kenya rolled tanks and troops across the border to fight the Shebab.
MSF immediately distanced itself from that operation.
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