Daystar Christian Centre in Lagos gave the money to the UNHCR team at a brief ceremony on Tuesday.
Mr Jose Antonio-Canhandula, UNHCR's Nigerian representative was quoted as saying during the service that the donation would be used to provide life-saving emergency assistance to families forced to flee their homes.
"Nigeria is unfortunately affected by this phenomenon, not only in North-East, but also the Middle Belt," he said.
"Many displaced persons do not have anywhere to sleep; no access to water; and access to healthcare facilities is very limited.
"They do not participate in the economy and cannot fend for themselves."
He also said he hoped the church's contribution would encourage other churches and organisations to help people fleeing conflict.
The church's senior pastor, Sam Adeyemi, explained why the church decided to donate the money.
Homelessness has no religion. Highlights from our partnership event with the @UNHCRNigeria towards helping Internally Displaced Persons (IDPs) across Africa. #DaystarUNHCR #DaystarNG pic.twitter.com/5IUWBwJf4R— Daystar (@DaystarNG) April 3, 2019
"When people flee their homes and leave everything they own behind, their needs become critical and their coping mechanisms compromised," he said.
"Without help, they cannot access shelter, or even cooking utensils - let alone education and healthcare.
"Some arrive with severe trauma after facing unimaginable ordeals before and during flight.
"We at Daystar are happy to support UNHCR's work on the ground to provide emergency relief and support to our forcibly displaced brothers and sisters."
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