The latest break-in occurred on Monday night when thieves broke through window bars and smashed the glass to enter a room in the Musée d'Horlogerie du Locle, Swiss media reported on Tuesday.
Among the 15 items stolen were modern wristwatches, travel clocks and antique pocketwatches, Neuchâtel police confirmed.
The burglars took less than a minute to carry out the theft, before fleeing by car, according to investigators.
No one has yet been apprehended.
It's the second museum in Switzerland's historic watchmaking valley to have suffered a burglary in a matter of months after the Musée International d'Horlogerie in La Chaux-de-Fonds was targeted at the end of May.
In that case, robbers used a car to ram the front door, before stealing watches from the entrance hall.
For the moment, police haven't established a link between the two.
It's been a bad week for Le Locle, where around 1,000 residents have been affected by a norovirus which contaminated the water supply.
Watchmaking has been a major industry in the Jura region of Switzerland since the 17th century.
The towns of Le Locle and La Chaux-de-Fonds developed in line with the industry's needs and their historically significant architecture has UNESCO World Heritage status.