The routes are Chalerm Maha Nakhon expressway with 19 tollgates, Si Rat expressway with 31 tollgates and Udon Ratthaya expressway with 10 tollgates.
Toll fees will be waived for 24 hours from midnight on Wednesday.
Makha Bucha is an important Buddhist holiday in Thailand with most people visiting temples and taking part in rites including a late-night candle procession.