The home side defeated St Joseph in the previous round of the qualifiers, while the visitors will take to the field for the first competitive game this term.
Match preview
Slavia Prague kicked off their league campaign on the back foot courtesy of a 1-0 defeat against Hradec Kralove at the Lokotrans Arena.
Following a drab opening half, Jindrich Trpisovsky's men fell behind to Daniel Vasulin's within 10 minutes of the second half which turned out to be the decisive moment.
The Slavists sit 13th in the league table after the opening round of matches and will be looking to get back to winning in their next league outing.
Before then, a third-ever meeting awaits against a Panathinaikos side who have won each of the last two encounters between the teams which both came back in 2001.
Off the back of a seven-goal haul in their last home outing, Thursday's hosts will be looking to turn on the style in front of their supporters once again.
Panathinaikos wrapped up their preparations for the upcoming campaign with a 2-1 victory over Dutch outfit Volendam at the Apostolos Nikolaidis Stadium on Thursday.
Goals in either half from Dimitrios Kourbelis and Carlitos Lopez got the job done for Ivan Jovanovic's men in a keenly-contested affair.
The Greens have now stretched their unbeaten run to six games across all competitions dating back to last season and have recorded five clean sheets in that time.
Ahead of the return leg in Athens a week later, Thursday's visitors will be looking to secure a positive result on the road and give themselves of a good chance of going through.
Slavia Prague Europa Conference League form:
Slavia Prague form (all competitions):
Panathinaikos form (all competitions):
Team News
With five goals in his last three appearances on home turf for Slavia Prague, 25-year-old Ewerton is definitely one to keep an eye on here.
Srdjan Plavsic missed the hosts' last outing through a one-game suspension, but the midfielder is now eligible to feature once again.
The duo of Jan Boril and David Hovorka are both sidelined for Thursday's contest, while Yira Sor also continues his spell on the sidelines.
Fotis Ioannidis was forced off with a knock in the first half of Panathinaikos' victory over Volendam, making the Greece U-21 international a doubt for this one.
Carlitos Lopez came on for Ioannidis in the aforementioned game to score the winner which could see him rewarded with a place in the starting lineup.
Slavia Prague possible starting lineup:
Mandous; Dorley, Eduardo, Ousou, Doudera; Tiehi, Holes; Ewerton, Traore, Usor; Jurecka
Panathinaikos possible starting lineup:
Lodygin; Kotsiras, Ganea, Magnusson, Schenkeveld, Vagiannidis; Cerin, Alexandropoulos, Kourbelis; Lopez, Kampetsis