The story was that a younger version of Ecco went to see the Big Blue, completing tasks such as herding seahorses, swimming through rings, and finding lost balls for sea lions along the way. The gameplay is similarly controlled to the original Ecco the Dolphin games, but mainly revolves around using these abilities for solution of simple puzzles and problems. One key difference is that the player cannot die in this game, so unlike in the original games, cannot drown by staying underwater too long. Likewise, creatures that appeared as enemies originally (Such as Sharks and Octopi) now appear in the background, and do not hurt the player. Two other playable characters were introduced: Tara the baby orca (there is also a bottlenose dolphin character named Tara in Ecco: The Tides of Time) and Kitnee the young Atlantic dolphin, who is darker gray than Ecco. They were interchangeable with Ecco and each other at any time.

Every character in Ecco Jr. has a different voice but not much else is different between them. The game features a password system, though all the passwords are included in the instruction manual. Ecco Jr. also features a "Parent's Menu" that had, among other things, a difficulty settings menu, level selection option, and facts about real dolphins.

A slightly modified port of the title, called Ecco Jr. and the Great Ocean Treasure Hunt!, was also available on the Sega Pico.

Ecco Jr. was eventually released on the Sega Mega Drive in Australia, the only PAL version of the game, November 1995. In November 2007, it was released in Japan for the first time ever via the Wii's Virtual Console. The game made its European debut August 2008 via the Virtual Console. Ecco Jr. was featured in the Sega Genesis Collection for PlayStation 2 and PSP.