Pekalongan sits on Java's north-coast transport corridor between Cirebon and Semarang. The railway station is served by regular trains west toward Jakarta and Cirebon and east toward Semarang and Surabaya.
By road, the city lies on the Pantura north-coast route and is connected to the Trans-Java toll road through the Pemalang-Batang section. Trains are usually the calmer way to arrive.