Rune Factory 2: A Fantasy Harvest Moon has gameplay similar to its predecessor. The game runs on its own clock and calendar; while the player is outside, one in-game minute passes every second. All four seasons are included with 30 days per season and weather varies each day.
The player begins with two tools, the hoe and the watering can, allowing the player to till the land and grow various plants after the player purchases or obtains seeds. Each type of seed has a different growth rate and cost, and some plants can be harvested multiple times. In the beginning of the game, the player is given a farm littered with rocks, stumps, and various objects littered throughout. Once the seeds are sown, the player must water them daily, after which they will be able to be picked and either sold, given away, eaten, or stored. Most plants are planted in one particular season (e.g. a spring plant will die in the ground during summer). They can be grown in certain areas outside the farm, where the climate is unchanging, but the player must water these areas that usually contain enemies.
The player interacts with objects and citizens through dialogue similar to a visual novel, including representing the townfolk with anime-styled images to narrate the story. In addition, cut scenes occur at certain points in the storyline. While every NPC has "Friend Points" that can be increased by visiting them and giving them items, seven bachelorettes also have a statistic called Love Points that increases as the player shows them affection. When a bachelorette has 10 Love Points, Kyle can marry her and raise a child who becomes the secondary playable character. His child cannot marry, but can conduct a pretend wedding instead.
The player has two types of statistics: ability and battle. The former show how well they can execute a certain task, while the latter are standard role-playing game statistics. These battle statistics can be improved either by defeating enough enemies to level up or by equipping a particular weapon or piece of equipment. The player's skills include basic tasks such as farming, fighting, and mining. A specific tool is usually required for every task, with some also being able to be used as weapons.
While exploring, the player can fight monsters to increase their strength or befriend and keep them as livestock, farmhands, as well as battling companions. Items harvested from livestock kept in barns can be sold for money or used to cook.