Edelaraudtee operates around 12 trains a day from Tallinn to Rapla, of which up to eight continue to Lelle, where the line divides. Two trains a day continue to Pärnu, and up to five to Türi of which up to three continue to Viljandi.
The journey time from Tallinn to Pärnu is 2h40m. Following completion in 2012 of an upgrade of the line from Türi to Viljandi to allow 120kmph running  the journey time to Viljandi has been reduced by 20 minutes to 2h22m. 
Edelaraudtee operate four to five trains a day from Tallinn to Tapa (from where the line to Rakvere and Narva diverges), Jõgeva & Tartu, with an additional return journey between Jõgeva and Tartu running outside summer months. Two journeys in each direction stop at all stations, taking around three hours to complete the journey. The remaining services are expresses calling only at Ülemiste, Tapa, Tamsalu & Jõgeva and taking around 2h15m to complete the journey. 
A morning service from Tartu to Orava & Koidula and return afternoon journey operate daily during the height of summer and at weekends off season. On Mondays to Saturdays there is an early morning journey from Koidula and Orava to Tartu, and a return journey in early evenings departs on Mondays to Fridays and Sundays.
There are two return journeys from Koidula to Piusa, operating daily during the peak summer period and at weekends off season. One journey to Piusa connects with the morning service from Tartu and one return journey connects with the afternoon service to Tartu.
Koidula railway station opened in September 2011, and is a few yards from the border with Russia border and the railway station at . Currently however there are no cross-border passenger trains, and services from Pskov to Pechory do not connect with the Edelaraudtee services in Estonia. 
On 16 March 2012 Edelaraudtee launched new information display solution based on GPS, that will provide passengers via Internet and physical displays real-time information on the trains’ locations. The developed information project, whose part is that solution, has an objective to provide passengers necessary opportunities to acquire trip information. Edelaraudtee has plans to equip all serviced train stations and stops with QR codes to link passengers with relevant station’s or train stop’s information display in Internet.