Below are nine decks for the Base & Jungle format. For a more complete 1999, experience, I recommend adding the Fossil set.
- Alakazam/Mr. Mime
- Clefable/Hitmonchan/Dodrio
- Haymaker
- Hitmonchan/Charmander/Dodrio
- Hitmonchan/Mr. Mime/Dodrio
- Hitmonchan/Scyther/Rapidash
- Lickitung/Scyther
- Venusaur
- Wigglytuff/Electabuzz
- Fun Match-ups
Below are eight of my favorite decks for the Base & Jungle format. Though most of them will seem straight-forward, the format itself can be tricky to learn, as it places a huge emphasis on preserving cards for the right moment.
Alakazam/Mr. Mime 
🌠 Iconic Deck
| Pokémon (19) | Trainers (24) | Energy (17) |
| 4x 3x 3x 3x 2x 2x 2x | 4x 4x 3x 3x 3x 2x 2x 1x 1x 1x | 9x 4x 4x |
Alakazam’s Damage Swap heals Mr. Mime, making it impossible to KO as long as its Invisible Wall Pokémon Power is working. Chansey and other high-HP Basics serve to absorb damage, while Scyther works as an alternate attacker to deal with the Psychic-resistant Pokémon Mr. Mime can’t damage. Though you’ll win many games by running your opponent out of cards, this deck definitely has the capability to draw six prize cards.
Clefable/Hitmonchan/Dodrio 
| Pokémon (17) | Trainers (27) | Energy (16) |
| 4x 3x 3x ERRATAMetronome must still do anything required to use the attack, such as discarding Energy cards.
Click to view Errata Page3x ERRATAMetronome must still do anything required to use the attack, such as discarding Energy cards.
Click to view Errata Page3x 1x | 4x 4x 4x 3x 2x 2x 2x 2x 2x 1x 1x | 12x 4x |
Both Clefable and Hitmonchan can launch effective attacks for a single Energy, which make them great against Energy Removal & Super Energy Removal. But since both of these Pokémon can be stumped easily (Hitmonchan by Fighting-resistant Pokémon and Clefable by weak attackers), you’ll need a way to easily switch them out. That’s where Dodrio’s Retreat Aid comes in handy, allowing you to easily find the right attacker for the moment. With this easy ability to retreat, you can move damaged Pokémon to the Bench, then use Pokémon Center to heal multiple Pokémon at once.
Haymaker 
🌠 Iconic Deck
| Pokémon (10) | Trainers (34) | Energy (16) |
| 3x 3x 3x 1x | 4x 4x 4x 3x 3x 3x 3x 3x 2x 2x 2x 1x | 8x 6x 2x |
Fast and aggressive, this iconic deck uses 4 PlusPower and 3 Gust of Wind to put immediate pressure on the opponent. Scoop Up not only allows you to heal your 70 HP Basics, but also bail out Hitmonchan anytime it comes across a Fighting-Resistant Pokémon. Able to attack for one Energy, the deck can withstand Energy Removal & Super Energy Removal.
Tip: Play Lass immediately before Jabbing a Fighting-weak Electabuzz, preventing your opponent from denying a KO with a timely Scoop Up or Switch.
Hitmonchan/Charmander/Dodrio 
| Pokémon (16) | Trainers (28) | Energy (16) |
| 3x 1x 3x 1x 4x 3x 1x | 4x 3x 3x 3x 3x 3x 3x 3x 1x 1x 1x | 9x 6x 1x |
Using Dodrio’s Retreat Aid, you can easily switch out your Fighting-type Pokémon to Charmander or Charmeleon when you face Scyther. With a PlusPower, Charmander’s Ember will give you an easy one-hit KO.
Hitmonchan/Mr. Mime/Dodrio
| Pokémon (16) | Trainers (30) | Energy (16) |
| 3x 1x 1x 4x 4x 3x | 4x 4x 4x 3x 3x 3x 3x 1x 1x 1x 1x | 9x 7x |
Other than Charmander, another good partner for your Fighting Pokémon and Dodrio is Mr. Mime. Though Mr. Mime isn’t as effective at dealing with Scyther as Charmander, it is stronger against other Hitmonchans you may encounter.
Hitmonchan/Scyther/Rapidash 
| Pokémon (13) | Trainers (29) | Energy (18) |
| 4x 4x 2x 2x 1x | 3x 3x 3x 3x 3x 3x 2x 2x 2x 2x 1x 1x 1x | 8x 6x 4x |
Another Haymaker variant, this deck uses Rapidash’s Stomp to deal with Scyther.
Lickitung Scyther 
🏆 Top Deck
| Pokémon (12) | Trainers (31) | Energy (17) |
| 4x 4x 2x 2x | 4x 4x 4x 4x 4x 3x 3x 2x 1x 1x 1x | 7x 6x 4x |
Constant Tongue Wrap attacks alongside a 4/4 Removal line will leave your opponent struggling to attack. Any damage your opponent does manage to do can be erased by Pokémon Center and Scoop Up, while Scyther shuts down any attempt to exploit Lickitung’s Fighting Weaknesses.
Tip: If your opponent starts to play passively, putting you in danger of decking out first, switch gears and go aggressive with attacks like Meditate and Slash.
Venusaur 
| Pokémon (22) | Trainers (23) | Energy (16) |
| 4x 4x 3x 3x 3x 3x 1x 1x | 4x 4x 3x 2x 2x 2x 2x 1x 1x 1x | 14x 2x |
Kangaskhan’s Fetch will help you evolve Bulbasaur all the way to Venusaur as you accumulate Energy in play. After securing Venusaur and four Grass Energy, you can begin launching either Comet Punch or Solarbeam attacks. Venusaur’s Energy Trans then allows you to use Pokémon Center to heal your Pokémon without losing any Energy cards, while Dodrio’s Retreat Aid will help Venusaur retreat when in trouble.
Tip: When attempting to power up a Solarbeam, use Energy Trans to spread your Energy cards out to 1 per Pokémon. This will weaken your opponent’s Super Energy Removal.
Revised on 5/8/2022: –1 Scyther, –2 Computer Search, –1 Professor Oak, –1 Pokémon Trader, –1 Gust of Wind, –1 Super Energy Removal, +1 Ivysaur, +1 Chansey, +4 Bill, +1 Energy Retrieval
Wigglytuff/Electabuzz 
🏆 Top Deck
| Pokémon (12) | Trainers (31) | Energy (17) |
| 4x 3x 2x 3x | 4x 3x 3x 3x 3x 3x 3x 2x 2x 2x 2x 1x | 8x 5x 4x |
With a full Bench and a PlusPower, Wigglytuff’s Do the Wave can hit for a devastating 70 damage, landing a one-hit KO on the format’s most popular Pokémon. Lass helps protect Wigglytuff from Energy Removal & Super Energy Removal, allowing you to keep the big attacks coming.
Tip: Lead with Electabuzz, baiting some of your opponent’s Energy Removal & Super Energy Removal cards. This gives your Double Colorless Energy a better chance at not being immediately discarded later in the game.
Fun Match-Ups
Looking to try the Base & Jungle format out with a friend and want a match-up that is close to even and fun to play? Here are some of my favorites: