Shinobi no Ittoki

both are about ninja wars in the modern world, including ninja disguised as high school students 

Ordinary dude finds out he's actually an heir to a really important and powerful family and must train to get stronger. There is also a girl who is tasked to watch over him and protect him. A lot of action plus ecchi. 

main characters world gets flipped upside down one day after almost getting killed by witches and is now being protected by the most popular girl in school 

A show about a unique fighting school where an overly naive and ingenuous protagonist goes to study? Check. Representatives of different industrial and political clans study at the school, who turn the school for political ambitions and clarifications, whose version of a specific weapon is better? Check. A technology race with allusions to corporatism and the Cold War? Check. Is the MC paired with another character, with whom they has an imbalance in power dynamics and an unspecified platonic or romantic relationship? Check. In the future, the show turns into a political action thriller, where everyone forgot about the lessons? Of course. 

Both are bad anime and I personally think they are not funny, but if you liked you liked one you might like the other as well. Both are ninja action anime taking place in the modern day. Difference is that one has a male character that just learned he is a ninja, while the other is a female who is a very experienced ninja.  

The same clans fight each other, but the setting is in the past.