Pokémon Gold and Silver take place in Johto,a fictional region modeled after the Kansai and Tokai regions of Japan. This is one distinct region of many shown in the various Pokémon video games. It features a total of seven cities and three towns, along with different geographical locations and Routes connecting most locations to one another. Some areas are only accessible once the player learns a special ability or gains a special item; for instance, the player must acquire the HM Surf, which allows the character to ride certain Pokémon across the sea, in order to reach Cianwood City

The silent protagonist of Pokémon Gold and Silver, called Gold, is a young boy who lives in New Bark Town. At the beginning of the games, players may choose either Chikorita, Cyndaquil, or Totodile as their starter Pokémon from Professor Elm.In addition, his rival Silver will steal a Pokémon from Professor Elm and become the protagonist's rival, battling the player at certain points in the game to test the player's Pokémon.

The basic goal of the game is to become the best trainer in all of Johto and Kanto; which is done by raising Pokémon, completing the Pokédex, defeating the eight Gym Leaders in Johto for Gym Badges, and challenging the Elite Four and the Champion, and then defeating the eight Gym Leaders in Kanto. Finally, the player may face off against Red atop of Mt. Silver.Also throughout the game, the player will have to battle against the forces of Team Rocket, a criminal organization that abuses Pokémon.

Like Pokémon Red, Blue, Yellow, and many other console role-playing games, Pokémon Gold and Silver are in third-person perspective, with players directly navigating the protagonist around the fictional universe, interacting with objects and people. As the player explores this world he or she will encounter different terrains, such as grassy fields, forests, caves, and seas; in which different Pokémon species reside. As the player randomly encounters one of these creatures, the field switches to a turn-based "battle scene," where the Pokémon will fight.

There are two main goals within the games: following through the main storyline and defeating the Elite Four and Red to become the new Champion,and completing the Pokédex by capturing, evolving, and trading to obtain all 251 creatures. A major aspect of this is developing and raising the player's Pokémon by battling other Pokémon, which can be found in the wild or owned by other Trainers. This system of accumulating experience points and leveling up, characteristic and integral to all Pokémon video games, controls the physical properties of the Pokémon, such as the battle statistics acquired, and the moves learned.

While Pokémon Gold and Silver retain the basic mechanics of capturing, battling, and evolving introduced in Pokémon Red and Blue, many new features were added. For instance, a time system was introduced, which makes use of a real-time internal clock. At the beginning of the game, the player inputs the time of day, the day of the week, and whether it is daylight saving time. Pokémon appearances are influenced by time of day: Morning, Day, and Nite. For example, the owl Pokémon Hoothoot will only appear at night. Special events are also determined by the day of the week, such as the bug catching contest, which is held in Goldenrod City's national park on Tuesday, Thursday and Saturday. In addition, certain Pokémon actions will only happen at specific times in the day; for instance, a happy Eevee will only evolve into Espeon in the morning and day time, and Umbreon at night.A new item called the Pokégear was introduced, functioning as a map and phone, allowing the player to call their mother, Elm, and other trainers who offer their phone number. Some trainers will call for a rematch and a few will call about rare Pokémon being seen that can be caught.

A variety of new items were also introduced in Pokémon Gold and Silver. Some are designed to exploit a new mechanic; Pokémon being able to hold items.Some held items restore health or cure status effects, such as Berries, a new set of items introduced in these games. Others can give boosts to the Pokémon, such as the Miracle Seed, which increases the power of Grass-type attacks. More specialized Poké Balls were also introduced, such as the Lure Ball, which is more effective if used against a Pokémon encountered with a fishing rod. To obtain these, Apricorns must be picked from special plants found throughout Johto, and a man in Azalea Town will fashion these into the different balls based on their color.

The games also introduce Raikou, Entei, and Suicune; a new type of legendary Pokémon that will wander around all of Johto,changing locations frequently. They can be tracked by the Pokédex once encountered, and will always attempt to flee, but will retain any HP loss and status effects. In addition, shiny Pokémon are first introduced in these games. These Pokémon have a different coloration than normal Pokémon of their species, and appear very rarely.

Two new Pokémon types were introduced, the Steel-type and the Dark-type.Steel-type Pokémon are known for their very high defense and resistance to many other types, while Dark-type Pokémon are immune to Psychic-type moves and are strong against Psychic and Ghost-type Pokémon. These two types serve to balance the Psychic-type; in the first generation games, its only weakness was the Bug-type, which lacked powerful offensive moves. In Pokémon Gold and Silver, more powerful Bug-type moves, among many others, were added. However, Pokémon knowing the new moves are not allowed to be traded to the first generation games. To solve this, a move deleter was introduced, capable of erasing any move known by the Pokémon, including HM moves, which previously could not be unlearned once taught to a Pokémon. In addition, several moves had their types changed, and some type match-ups were changed as well. For example, Ice-type moves were made ineffective against Fire-type Pokémon, when they previously did normal damage. Another major change from the original series was the splitting of the Special stat into Special Attack and Special Defense, which increased aspects of strategy.

With the introduction of Pokémon breeding, all Pokémon are assigned to one or two breeding groups. When a male and female Pokémon that share at least one breeding group are left at a Pokémon Daycare, they may produce an egg, which will hatch into a young Pokémon. Another way to produce an egg is by breeding any Pokémon with a Ditto, which is genderless and will mate with any Pokémon capable of breeding. The young Pokémon will inherit the species of its mother (or non-Ditto parent in the case of Ditto breeding), and certain moves from its father, which can be inherited in a variety of ways. Legendary Pokémon and Baby Pokémon, among certain other species, cannot breed.