The 24-year-old was placed in Heat 4 of Tuesday’s contest but endured a poor start which ultimately cost him qualification to the semi-finals.
Stacey’s time of 51.12 seconds saw him secure the last but one position in his Heat, which was won by Cypriot swimmer Nikolas Antoniou.
The Ghanaian had booked his place at the Olympics via the wildcard route and went into the competition with a personal best of 50.57 seconds, having competed at the 26th Easter International Swim Meet in Malta.
Harry Stacey looks to the future after disappointing Olympic debut
He is also Ghana’s current national record holder in the Men's 100m Freestyle and was the fastest among the competitors prior to competing in his Heat despite falling short.
In an interview earlier this year, Stacey said he was aiming to give his best at both the African Games and the Olympics.
“My goals as an athlete have always been to be my best self and see how far I can go in the sport that is swimming,” he said.
“Representing Ghana on the international stage, I hope to compete at the African and Olympic Games this upcoming 2024 Summer. With the help of a college swim program, I'd hope to take my abilities to new heights and become a top 20 athlete in the world for my respective events."
Meanwhile, speaking to the Ghana Olympic Committee after finishing seventh in his debut Olympics challenge, Stacey said he was already looking to qualify for the next Olympics.