The incident occurred on Saturday in a ranch to the south of Nairobi National Park.
The attack was witnessed by another teenager, who raised the alarm, the KWS said in a statement.
"KWS rangers and response teams were swiftly mobilized and traced bloodstains leading to the Mbagathi River, where the girl's body was recovered with injuries on the lower back," the conservation agency said in a statement.
"The lion was not sighted at the scene," it added.
It said a trap had been set for the lion and teams deployed to comb the area, along with additional safety measures.
The KWS said a 54-year-old man had also been killed by an elephant in Kenya's Nyeri County on Friday.
"KWS conveys its heartfelt condolences to the bereaved families and continues to work closely with local law enforcement and communities to enhance the safety of people living near protected wildlife areas," it said in the statement.
It called for more investment in "human-wildlife conflict mitigation", including early warning systems and greater collaboration with affected communities.
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