Charles Nyachwara had been charged with murder, but escaped and set up a new church in Mbale town.
Police in Uganda worked with their Kenyan counterparts to arrest the pastor on the his wedding day.
The schoolgirl was five months pregnant after a year-old relationship with the pastor when she was killed.
The student, 17, was a Sunday school teacher at a church the pastor was leading before he escaped.
After the student confessed to her parents that the clergyman had impregnated her, the matter was reported to the police who arrested and arraigned the pastor at the Kitale Law Court.
He was charged with defilement and was released on bond.
The pastor reportedly intercepted the student as she returned home after attending antenatal clinic at Kitale District Hospital, and killed her.
On the fateful day, the two met at Kibomet Africa Inland Church where the girl found the pastor waiting for her.
They talked and then as the student left to board a matatu, she was allegedly stabbed several times by the pastor. The pastor then fled into a maize plantation but was arrested by a watchman guarding a homestead.
The pastor underwent a psychiatric test and was arraigned in Kitale Law Court where he was charged with murder.
Zacharia Ogechi, a kin to the cleric, deposited a title deed for his land worth Sh1 million as surety for the release of the pastor.
However, Nyachwara failed to appear for his trial on several occasions prompting the then judge Joseph Karanja to summon Ogechi to explain the whereabouts of the accused person.
Ogechi told the court the pastor had gone underground and pleaded for time to trace him. And for over five years, Ogechi has traversed Tanzania and Uganda in search of the fugitive.
Ogechi’s tireless journey started in Mombasa in 2012 where he tracked the pastor with the help of the police.
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However, the pastor got wind he was being sought and escaped to Mwanza in Tanzania.
“I visited several areas in Tanzania such as Mwanza, Panda and Silale looking for him, but I didn’t succeed because he had moved to Uganda,” Ogechi told journalists in Kitale.
In Uganda, Nyachwara settled in Mbale District and changed his citizenship before establishing a church in the area.
Nyachwara was planning to wed with his Ugandan fiancee when Ogechi discovered and alerted the police.
The police on Friday presented Nyachwara to court where Ogechi withdrew his surety and was handed back the title deed. Ogechi heaved a sigh of relief when the court handed him back his title deed.
Trans Nzoia County Commander Lillian Okembo said the pastor will remain in custody until the matter is determined.
“I have spent a lot of money to trace the pastor and I’m happy that I have got my title deed back,” he said.
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