Although the number of magazines publishing Christian short stories has shrunk lately, a few are still around and open to submissions from writers. Here are the ones I know of, including several that are perhaps best described as Christian-friendly, since they are not aimed only at Christians.
Clubhouse (children's, open to some speculative)
Clubhouse, Jr. (children's, general fiction)
Kids' Ark (children's, open to some speculative)
Primary Treasure and Our Little Friend (children's, true stories)
Ruminate (general fiction)
Splickety (general fiction, including historical)
Ancient Paths (most genres, including some speculative)
The Common Oddities Speculative Fiction Sideshow (speculative)
TRC (all genres, including speculative)
TWJ (all genres, including speculative)
The Untold Podcast (speculative)
Also, the Splickety Blog, while not a magazine, publishes stories in all genres, including speculative.
Do you know of any other magazines that publish Christian fiction?