Palazzo Pretorio is located in Piazza del Comune, in the historic center of Prato, an easy walk leads to the Porta al Serraglio station (500 mt), Central Station (1200 m) and links to the main urban and suburban buses.
By car
A11 Firenze - Pisa, exit Prato est; follow signs to the center. There are paid parking near the museum, the closest one is in Piazza San Francesco. Others, large and fairly close, are Mercatale Square, Piazza del Mercato Nuovo and under the Porta al Serraglio station.
By bus
Autolinee Toscane buslines provide a service linking Florence and Prato with departures every 15 minutes from Piazza Vittorio Veneto, near the railway station of Firenze Porta al Prato. 
Info: https://www.at-bus.it/it/linee-e-orari/prato

To learn more about how to get to Prato: Towards Prato