The charity said it can be tempting to pray that the secretive state's dictator is dethroned but, if Kim falls, others will take his place.
Dr Eric Foley, a Release partner who works with North Korean refugees, said: "I have never encountered a North Korean Christian who has prayed for the regime to be overthrown, not once in 15 years. Underground Christians are praying that Kim Jong-Un will come to know Christ.
"Perhaps North Korean Christians know better than the rest of us, that it is not a change of government that will bring peace, but the entry of the Prince of Peace into our hearts.
"We should follow their lead and pray not for regime change, but for a change of the heart of the regime."
A call for prayers for the leader's salvation came after North Korea announced plans to stage a pre-Olympic military parade.
The nation will stage its annual display of thousands of troops, tanks and missiles on 8th February, the day before the Winter Olympics gets underway across the border in South Korea.
The muscle-flexing has been described as grandstanding in a crisis that could threaten nuclear war, but Release International said that crisis should be turned into a rallying cry for prayer for the persecuted.
Paul Robinson, CEO of Release International, said state surveillance of Christians in North Korea has never been tighter.
"North Korea is probably the harshest persecutor of Christians on the face of the earth," he said.
"The world may feel on a knife-edge with nuclear missiles pointing in every direction, but the threat of extermination is the daily reality for North Korean Christians.
"North Korea doesn't just persecute Christians, it executes them. This crisis should give us the impetus to pray for the persecuted in that country."
There are an estimated 100,000 Christians in North Korea. Release said among them, 30,000 have been rounded up into concentration camps, on charges of sedition and conspiracy against the state.
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