RPG Maker 2003 allows developers to adjust the playback speed of an area's background music, something that Yume Nikki frequently makes use of. Several songs are featured in multiple areas, and in most cases, they are slowed down or sped up to fit a certain mood:

• The Mall Rooftop's background music is "I Fly to the Sky Forever", the Witch's Flight music, played at 70% speed.
• The Sewers' eponymous background music is "A Damp and Humid Place", the Dense Woods A music, played at 60% speed.
• "Menu Type Change", the background music for each of the rooms in the Mall, is "Start of Yume Nikki", the title screen theme, played at 50% speed.
• The eponymous discordant noise heard when summoning Uboa in Poniko's house is the screeching that plays in the Guillotine Room slowed to 50% speed.
• "I Don't Know Where I Came From", the Teleport Maze's background music, is "FEVER", the Aztec Rave Monkey's theme, played at 50% speed.
• "On a Hill, Shining Feet", the Neon Tile Path's background music, is the Snow World's eponymous theme played at 70% speed.
• "Wei Wilderness", the Wilderness' background music, is "The Dream Always Begins in the Veranda", the ambient noise heard in the dream version of Madotsuki's apartment, played at 50% speed.
• The Face Carpet area in the Forest World uses "Tokun-Tokun", the background music from the hot springs building hidden in the Wilderness, played at 70% speed.
• The background music heard in the entrance to the Mall is the eponymous background music from Shield Folk World, played at 50% speed.
• The Docks' eponymous background music is "The Mural World", heard in the area of the same name and in Footprint Path 1, played at 50% speed.
• Puddle World's eponymous background music is "Many Footprints", Footprint Path 2's background music, played at 50% speed.

Additionally, many unique area themes are played at a modified speed by default:

• "Scar Doesn't Disappear", the background music that plays in the underground area in Mars, is played at 80% of its actual speed.
• "The Land of Dreams?", the Pink Sea's background music, is played at 60% speed.
• "The Scribbling World", the ambient hum heard in Graffiti World and Hell, is played at 60% speed.
• "The Candle World", the ambient noise heard in the area of the same name, is played at 50% speed.
• "Do You Play a Family Game?", the main menu theme for the "Famitendo" in Madotsuki's room, is played at 70% speed.
• "The Black Department Store", the ambient noise heard in the Mall and in Big Red's room, is played at 50% speed.
• "The Forest World", a series of gong chimes heard in the area of the same name, are played at 50% speed.
• "Up Up...", the ambient hum heard in the stairway leading from the Wilderness to the Sky Garden, is played at 50% speed.
• "The Wall of Cold Stone", the ambient noise heard in Ghost World, is played at 50% speed.
• "I Don't Want to See It!", the ambient noise heard during the FACE event, is played at 80% speed.
• "The Number World", the ambient noise heard in the area of the same name, is played at 50% speed.
• "A Small Shrine Was Forgotten", the background music for the FC Pyramids and other select areas in FC World, is played at 90% speed.

Relatedly to the above, the chimes that make up "The Snow World" are also the same ones heard when interacting with jellyfish, played back at 110% speed for the first note and at normal speed for the second.