Interesting question! I guess it depends on how recently a fic needs to have updated to considered to be "still updating", and if you start counting from the first chapter of the most recent reboot or the first chapter of the very original version.
The oldest published incomplete story in the main Pokemon section on Fanfiction.net which updated within at least the past year is
Anything But Ordinary, published July 18, 2002 and updated December 17, 2021. If you're looking for something that's long-running in the sense of having a lot of words and updating at least semi-regularly for
most of its runtime, you might want to look at the fifth oldest story,
Silver Resistance, published June 3rd 2008 and last updated November 2nd 2022. It's up to almost a million words, and (I believe, not 100% sure) has been updating at least occasionally throughout that whole time, barring a hiatus from August 2018 to October 2020.
I also made sure to check the crossover section for Pokemon, as well as the weird specific Digimon/Pokemon crossover category FFN has in the 'Misc Crossover' section, but nothing there was earlier.
Looking at some of the other major Pokemon archives:
On Archive of our Own, the oldest published fic in the "Pocket Monsters | Pokemon - All Media Types" category which updated within the last year appears to be
Gnosia Stella Coronae, published August 30th 2012 and updated September 4th 2022. Not surprising given how relatively new AO3 is.
On Serebii Forums, the story with the oldest publication date that updated within the past year was Obsession, but coming in second place with a listed date of October 2nd, 2011 and most recent update of September 28, 2022 is Chibi Pika's
The Legendarian Chronicles. However, I believe various versions of the story have been running since at least 2004 or so; you'd have to ask Chibi for more details.
On Bulbagarden forums, the longest runner updating within the past year is
How To Conquer Kanto In Eight Easy Steps, beginning October 5th 2010 and updating February 22, 2022.
On Pokecommunity, the oldest to have updated within the past year is
Star Performer, published Jan 8th 2018 and updated September 27th 2022. (I may have overlooked something, as Pokecommunity doesn't list publication dates on the main forum view, forcing me to check threads individually, but I doubt it would be much earlier than that.)
I suppose Dragonfree's
The Quest For The Legends might count if Dragonfree starts posting chapters for yet another revision, as I believe is her plan, given that the original version began June 19th 2002.
Of course, it's entirely possible that the
true longest-running Pokemon fic is actually hosted on some obscure fansite that's been running since 1999 or so...
