Yes, WhatsApp, FaceTime, and other video/voice calling apps work perfectly fine in Japan over mobile data.
Japan boasts a world-class mobile network infrastructure with excellent coverage across the country, including major cities like Tokyo, Osaka, and Kyoto, as well as popular tourist regions. Unlike certain other nations, there are absolutely no government restrictions or throttling on Voice over IP (VoIP) services here. This means you can freely make and receive calls, send messages, and enjoy high-quality video chats with friends and family using your preferred apps without needing any workarounds or a VPN.
When you use an eSIM for your trip, your device will automatically connect to the strongest available major network in Japan, ensuring reliable connectivity for all your communication needs. The exact network partner can vary by plan, but your VoIP apps will function normally.