The travel service provider will pay 1.4 billion pounds, mainly in cash, for the Edinburgh-based firm, they said in separate statements today.
NASDAQ-listed Ctrip, partly owned by Chinese search giant Baidu, provides online booking for airline and railway tickets as well as hotels, and describes itself as China's largest travel company.
It generated more than 350 billion yuan (USD 51 billion) in gross merchandise value last year, the firm said on its website, referring to a measure of online sales.
The acquisition took Skyscanner "one step closer to our goal of making travel search as simple as possible for travellers around the world", he added.
Skyscanner provides similar services to Ctrip and has 60 million monthly active users, mainly in Europe.
Ctrip co-founder and executive chairman Liang Jianzhang said: "This acquisition will strengthen long-term growth drivers for both companies. Skyscanner will complement our positioning at a global scale."
Skyscanner will remain operationally independent with its current management team, the statements said.
"The Skyscanner deal, as well as the buying of US travel agencies, is part of Ctrip's effort to expand its overseas business," Zhang Min, analyst with Shanghai-based consulting firm Business Connect China, told AFP.
"Ctrip is already the leader in the domestic market in both ticket and hotel booking, so its future growth lies in overseas expansion."
Average hotel rates were higher overseas, she added, so the deal would help improve Ctrip's margins.
The Skyscanner purchase, already approved by boards of both firms, is still subject to customary closing conditions and is expected to be completed by the end of 2016.
The deal gave Baidu, which controlled Qunar, a 25 percent stake in Ctrip.
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