In contrast to the original version, Oregon Trail II made an effort to include greater roles for women and racial minorities.

The CD-ROM came with an official strategy guide and certificate of authenticity, all packaged in a commemorative wooden storage box.

In addition, events such as diseases (including dysentery, measles, cholera, and others), obstacles on the path, accidents while traveling, and even interactions with other groups in one's wagon train involve being directed to choose a course of action from a set of multiple choices.

However, if the player settles at a destination other than the one they had selected at the start of the game, they will not receive a bonus, regardless of their chosen occupation.

Whenever an event (e.g. an accident or illness) happens, the game halts and the player must make a choice of action, so it is much more interactive than the previous version.

Outfitting the supplies and choosing the parties equipment in their journey becomes a possible point of player control leading to increased scoring chances.

One has the option of taking a computer generated "package deal", ostensibly offered by the trailhead town's merchants.

Conversely, some assets are only available by the package (e.g. chains, anvils, plows) or by trading, though many of those can be purchased from merchants or blacksmiths further down the trails.

Various points of the children's story are triggered when the player reaches a certain destination on the trail, which ranges from dangerous experiences (Jimmy is bitten by a snake) to campfire scenes where Captain Jed would tell a story that reflects other historically accurate incidents (e.g. the Donner Party, the California Gold Rush, and the Santa Fe Trail).

The soundtrack of Oregon Trail II has also been removed, replaced with a single repeating audio loop.