Simply put, Magic Pants are the "civilian" clothing the characters wear as they go about their daily business. They may lose them during the Transformation Sequence, but once the dirty work is done, they'll appear back in them often right where they were standing. This can even happen if the transformations are shown to explicitly destroy the clothing.
To be fair, it's not like a character suddenly conjuring up several hundred pounds of mass out of thin air is made any more unbelievable by their clothes being exempt.
Note that in many cases, even if the rest of his clothing is destroyed, the hero's pants will miraculously survive. You can thank the Moral Guardians for that. This is also conceptually related to Out-of-Clothes Experience: Your clothes technically aren't a part of "you", so in spirit-space you're naked. Monster Modesty (a monster walks around almost naked for little reason) is often used in conjunction with this trope.
Also note that Magic Pants are only for characters who seem to remain clothed even when it's inconsistent with what gives them their powers. Magical characters (who presumably can conjure up a fresh set), characters with super speed (Superman, The Flash) who have the demonstrated ability to get dressed faster than the human eye can see, or heroes whose clothing is what makes them super in the first place would actually be aversions of this trope.
For transformations which ruin clothing in such a way as to show a titillating swath of skin while still keeping the naughty bits covered, see Clothing Damage.
See also My Suit Is Also Super — for a transformation-powered hero, a popular kind of super-suit is one that can transform with them.
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- Axis Powers Hetalia fanfics Hakkōna and Kaitō Kokoro: When Kiku turns into human or nekomataneko form, he always has clothes on. This could be due to him literally creating the clothes, but still.
- Averted in one case for DC Nation. Fauna's clothing doesn't "keep up" when she shapeshifts. This led to her fighting off a zombie horde and only realizing AFTER she had come out of her Hulking Out that she was wearing nothing at all. The only saving graces to the situation were that she grew up on a hippie commune and that Hades had forced the Titans to compete in the nude, so she was in good company. She later designed (and sewed) her costume to accommodate her shapeshifting.
- Averted in With Strings Attached; Paul cannot wear clothing, as he rips through it easily, so he has to use a cosmetic illusion to remain modest—when he feels like it. He does walk around naked on occasion, though rarely in public. On the other hand, George's clothing explicitly goes into his "closet" when he changes, so he keeps a whole wardrobe in there and can put on any stored outfit, any time.
- Invoked in Avengers of the Ring, an Avengers/The Lord of the Rings crossover. During the Fellowship's meeting with Galadriel, Bruce receives a magical braise (a pair of silk boxer shorts) from her that works exactly as this trope suggests.
- Weaponized in Plan 7 of 9 from Outer Space. Mad Scientist Dr Zarkendorf tries to turn himself into an thirty-foot hulk with serious anger management issues, but his Crazy-Prepared enemy has arranged for his underwear to be made of unbreakable non-stretch fabric, causing Zarkendorf to pass out from the pain.
- Averted in I Guard the World when Tonks morphs into a troll to save Harry from his abusive relatives and the only clothing on her body post-change is a shred of skirt hanging around her ankle.