The U.N. mission was established in March after a peace agreement was signed between the Sudanese government and the southern rebel forces earlier this year.
Tokyo will send Foreign Ministry official Yusuke Kudo for a preliminary period of six months, assigned to the U.N. Mission Analysis Center in Khartoum.
Kudo will be the first Japanese civilian to participate in a U.N. peacekeeping mission since a Foreign Ministry official was dispatched to East Timor in September 2000.
Despite lingering security concerns, the Japanese government says it is eager to contribute to efforts to reconstruct Sudan, which was devastated by a two-decade civil war that killed over 2 million people.
Japan has pledged US$100 million (euro81.49 million) in development assistance, in addition to material assistance such as mine detectors, to assist the U.N. peacekeeping operation, which is set to begin in November.