Mostar and Jajce are both Bosnian towns with medieval old towns, dramatic water features, and significant historical weight. But they operate at very different scales and suit different kinds of travelers. For most short trips to Bosnia, the choice is not especially difficult once you understand what each actually offers.
The direct answer for most travelers
If you have a short trip to Bosnia and can only visit one of the two, choose Mostar. The Stari Most bridge is one of the most iconic sights in the Balkans, the old town has more depth and atmosphere than Jajce, and it connects more naturally with Sarajevo as a short Bosnia circuit. Jajce is excellent as a route stop but rarely the primary reason to visit Bosnia.
What Mostar offers
Mostar is built around one extraordinary centerpiece -- the Stari Most (Old Bridge), a 16th-century Ottoman arch bridge over the Neretva river. The bridge was destroyed during the 1990s war and rebuilt in 2004. The old town surrounding it -- the Kujundziluk bazaar street, the mosques, the river gorge below -- creates one of the most visually concentrated historic areas in the region.
Mostar works best with at least one overnight stay. The daytime version, when day-trippers from Dubrovnik and Split fill the old town, is significantly worse than the evening version when the crowds leave and the bridge is almost empty. See the overnight guide for more detail on timing.
Mostar is about 2.5 hours from Sarajevo by bus (roughly 10 EUR) and about 3.5 to 4 hours from Dubrovnik (roughly 15 EUR).
What Jajce offers
Jajce is built around a striking waterfall at the confluence of two rivers, an intact medieval fortress, and a genuinely quiet Bosnian small-town atmosphere. The Pliva Lakes a few kilometers outside town add a scenic secondary stop. The whole experience -- waterfall, fortress, lakes, old town -- can be covered in about four hours, which is why most travelers see Jajce as a route stop rather than a destination in itself.
Jajce is about 2.5 to 3 hours from Sarajevo by bus and sits naturally on the route between Sarajevo and Split (via Banja Luka) or between Sarajevo and the northwest of Bosnia.
When Jajce is the better choice
Choose Jajce over Mostar when: the route goes through northwest Bosnia anyway, the trip has already included Mostar on a previous visit, or the priority is a genuinely quiet off-the-beaten-path stop rather than an iconic widely-photographed sight. Jajce has almost no tourist infrastructure compared to Mostar -- the waterfall is striking and largely untouristed, which some travelers find more rewarding than the polished but crowded Mostar old town.
Can you do both?
Not easily on a short trip. Mostar and Jajce are not close to each other -- Jajce is about 3.5 hours northwest of Mostar by bus, and combining them requires either a car or a Sarajevo hub. The most practical approach for a trip that wants both is to use Sarajevo as a base: day trip or overnight to Mostar (south), and a separate day trip or overnight to Jajce (north). That works in four to five nights based in Sarajevo.