There are a handful of differences between the Rurouni Kenshin anime and manga. When it comes down to core of it all, both anime and manga series provide the same plot. The way the characters are introduced, their personalities, and the order of the episodes are all pretty much the same, with a few minor exceptions.

In the Rurouni Kenshin manga, there are no filler chapters, unless you count the bonus chapters in the earlier volumes. Thus, the animated episodes (13-18, 25-27, and 63-95) are all made for the anime only. The characters and storylines featured in those specific episodes are not featured in the manga.

Tokyo Arc

- Hiruma Brothers
Anime: Only Gohei exists. Gohei was formerlly a Kamiya Kasshin Ryuu student, expelled after he wanted to use his sword for killing, rather than protecting others. Gohei, by himself, assembled a group of lackies to help him bring down the Kamiya Dojo. Gohei makes two more appearences in the anime after he failing to get his revenge. Once to hire Zanza and the other to get revenge on Kenshin when he doesn't have his Sakabatou (Ep. 18). After that, he is never seen or heard of again.
Manga: Gohei is really stupid and has no relationship of being a past Kamiya Kasshin Ryuu student. He barely talks because he's the brawn, while his brother, Kihei, is the brains of the entire operation. Kihei poses as Kaoru's housekeeper, when really, he is plotting to have Kaoru sell the Kamiya Dojo to him. It is later discovered that Kihei wanted to sell the dojo off because of the high land price of it. Both Kihei and Gohei appear two more times in the manga. Once to hire Zanza and the other when confronted by Sanosuke in his home town.

- The Yahiko and Yamagata Switch
Anime: Yahiko is introduced in episode two. Yamagata is introduced in episode three.
Manga: Yahiko is introduced in chapter three. Yamagata is introduced in chapter two.

This is the only switch in the series.

- Yahiko's Savior
Anime: Kaoru goes to rescue Yahiko from the Shuei Gumi, but Kenshin comes to assist later.
Manga: Kenshin goes to deal with the Shuei Gumi by himself.

- Megumi's Return to Kanryuu/Sanosuke vs. Shikijou
Anime: Sanosuke tries to stop Megumi from returning to Kanryuu when he meets up with her at the gates of Kanryuu's mansion. Shikijou appears, causing a fight to occur. Sanosuke defeats Shikijou, but Beshimi kidnaps Megumi afterwards.
Manga: Sanosuke really dislikes Megumi for killing his friend with the opium she sold him. He does not try to stop her from returning to Kanryuu. Megumi simply goes to Kanryuu's mansion and is taken back as a prisoner. Thus, Sanosuke's fight with Shikijou takes place in the mansion, rather than outside.

- Raijuuta, Yutarou, and the Shinko Ryuu
This will be explained later after I have revised the manga once again.

- Yutarou's Comeback
Anime: Yutarou makes his return in the anime in episode eighty-three. It's not a very good comeback. He waits in the Kamiya Dojo and immediately begins sparring with Yahiko. He has brought a German doctor/professor along with him named Hans, and the whole thing leads into a ridiculous filler arc. (I have not watched it completely as of yet.)
Manga: Yutarou does not return until the very end of the manga. His name is seen on the Kamiya Kasshin Ryuu board under the assistant instructors' section along with Yahiko. As for what he looks like, it is unknown.

Kyoto Arc

- Misao's Meeting with Kaoru and Yahiko
Anime: When Kenshin leaves the Aoiya, Misao chases after him through the busy streets of Kyoto. At the same time, while on the look out for the rurouni hopefully to appear, Yahiko identifies Aoshi in the sea of people. He chases after the Oniwa Banshu's leader with Kaoru right behind him, only to collide head-on with Misao.
Manga: Since Kaoru and Yahiko were staying at the Shirobeko, the Akabeko's twin restaurant, they were forced to work in order to have a place to live for the while. Three days after Kenshin departed from the Aoiya, Misao entered the Shirobeko to have a meal and noticed a "wanted" poster made by Kaoru of Kenshin up on the wall.

- The Whereabouts of Hiko Seijuurou
Anime: After the incident with Chou, Okina is able to find out the location of Kenshin's master under a different name, and promptly gives it to the rurouni before he departs from the Aoiya.
Manga: Kenshin is called back three days after leaving the Aoiya to be given the location of Hiko Seijuurou by means of a signal flare.

- Owl's Torture
Anime: The sole member of the Owls that returns to Shishio's base in the Hiei Mountains to report the squad's failure of raiding the Aoiya Inn has boards nailed to him, almost as though he was crucified.
Manga: Because he won't break his code of silence when asked to answer some questions by the Oniwa Banshu members at the Aoiya, the Owls' member returns to base with burning hot candles and large nails to keep them in place melting on his hands; punishment only thought up by Okina himself.

- Aoshi Visits the Aoiya
Anime: This does not occur in the anime.
Manga: Aoshi returns to the Aoiya after years of absence only after he's made a mess of Okina. Basically, he wants to know the whereabouts of Kenshin so he can kill him, but no one gives in to his demands. Yahiko and Kaoru speak up for the frightened Oniwa Banshu members, leading Aoshi to just leave word with them all that he'll be waiting for Kenshin at Shishio's base.

- Houji's Trust
Anime: To find out if Houji is truly the one to blame for the failure of the Great Kyoto Fire, Usui asks him personally during a meeting between Shishio and all of the Juppon Gatana. When Houji lies that he is at fault, Usui bends back his left index finger.
Manga: Instead of simply beding back Houji's finger, Usui rips off seven of Houji's nails; seven being the number of Juppon Gatana members that would have been betrayed and left behind if the Great Kyoto Fire was a success.

- Usui's Death
Anime: Saitou uses the Gatotsu Zeroshiki and pins Usui up against a wall.
Manga: The Gatotsu Zeroshiki rips Usui in half, pinning his body from the stomach up on the wall.

- Revenge Arc
The entire arc is excluded from the Rurouni Kenshin anime. It is only available in the manga. For the reason why the Revenge Arc was never animated, please consult the FAQ.