Nerawareta Gakuen

Both deals with time traveling with a bit of romance mixed in. Both deals with the consequences of time travel. 

If you enjoyed Toki wo Kakeru Shoujo, you will likely enjoy Nerawareta Gakuen. Both stories deal with difficult concepts like personal connection and love and use time travel as a plot device to drive the story. Both stories contain average characters, who have difficulty understanding others let alone themselves. As far as visuals and audio, both contain beautiful visuals, heartfelt musical scores, and feature a wonderful cast of voice actors. 

•both have a time traveling sense •both are situated in schools and every day life, with the typical genres falling into place, comedy, romance etc. •both animation are individually spectacular and have their own uniqueness about it •both plots are absolutely different in a sense of 'flow' Toki wo..... is just brilliant within its confinements of story progression, where as Nerawareta just jumps from one topic to the next without any explanation whatsoever, it has alot of plot holes without being explained and you probably have to watch it twice just to understand alot of shit. •they are both similar with a character with time traveling purposes, also the genres. but to be frank i continued watching Nerawareta for its beautiful animation. you might like one if you like the other, but theres a big diff in the storyline/plot holes. read more 

The same very slow paced movement through the story. Romance everywhere. AND THEN ITS SADNESS TIME. 

In both works, a boy enters into a world that is new for him. There is a melancholy feeling infused and in both cases, we are asked to ponder this question -- must we 'move on' even if we are perfectly comfortable in our present surrounding? Nerawareta Gakuen is a movie with gorgeous visuals, but Angel Beats has a much better soundtrack. Both movies will make you feel a lot of feels.  

Both deal with people traveling trought time in order to change the actual future. And both have a somewhat weird pacing not suitable to everyone. 

1. The plot of each anime is about aliens coming to earth for some reason. 2. Both animes have 2 male and 2 female characters which the anime centers around and follows and at last 3. The story itself is very touching and many scenes are very alike.