Agogo was called up to the Ghana squad for the [[2008 Africa Cup of Nations]]. He played in the first game of the cup against Guinea, hitting the post with a header in the 20th minute and helping Ghana to a 2–1 victory. He then scored in the following game against Namibia, tapping home [[Michael Essien]]'s cross for the only goal of the game.
Agogo then netted another goal, the winner, a latean 84th minute goalwinner, in the [[2008 Africa Cup of Nations#Quarter-finals|quarter final]] against Nigeria after [[John Mensah]] had been shown a red card in the 60th minute.<ref>{{Cite web |date=22 August 2019 |title=Football News Ghana striker Junior Agogo dies at age 40 |url=https://www.eurosport.com/football/football-news-ghana-striker-junior-agogo-dies-at-age-40_sto7416442/story.shtml |access-date=26 July 2022 |website=Eurosport |language=}}</ref><ref name=":0" /> Ghana missed out on the final, however, and had to settle for a [[2008 Africa Cup of Nations#Third place match|third-place play-off]] against [[Ivory Coast national football team|Ivory Coast]], in which he scored again in a 4–2 victory.<ref>{{Cite web |last=Taylor |first=Chris |date=4 April 2008 |title=Junior show time |url=https://www.wsc.co.uk/the-archive/31-Players/4622-junior-show-time |access-date=26 July 2022 |website=When Saturday Comes |language=}}</ref> Alongside [[Sulley Muntari]] he was Ghana's top scorer in the competition, and the 5th highest scorer overall.
In total, Agogo scored 12 goals in 27 matches for the national team between 2006 and 2009.<ref>{{NFT player|id=8111|accessdate=}}</ref>
