Swiss side Thun, who sacked coach Urs Schoenenberger on Monday, gave themselves a fighting chance of progressing in the UEFA Cup after securing a 1-0 first-leg lead over Hamburg SV on Thursday.
English Premier League side Middlesbrough also put themselves in the driving seat in their first knockout round tie, winning 2-1 at VfB Stuttgart.
Thun's Brazilian Adriano fired home a cross from Pape Omar after half an hour to seal the victory.
Thun, who nine years ago were playing amateur third division football before crowds of around 100 people, sacked Schoenenberger on Monday citing "irreconcilable differences".
Schoenenberger had steered the tiny Swiss club to a shock place in this season's Champions League where they acquitted themselves well, finishing third in their group to earn a UEFA Cup place.
Middlesbrough, buoyed by their stunning 3-0 defeat of English champions Chelsea on Saturday, found themselves 2-0 up minutes after halftime in the Gottlieb Daimler Stadion.
They went ahead against the run of play when Jimmy Floyd Hasselbaink pounced on a defensive mistake in the 20th minute and Stuart Parnaby swept in a second in the 47th minute.
Dutch striker Hasselbaink went close to scoring a third away goal for Boro but Stuttgart gave themselves a lifeline four minutes from time with an unstoppable free kick by Serbian international Danijel Ljuboja.
"We would have settled for that before the game," Boro manager Steve McClaren told Channel Five. "You need to be disciplined and that was what we were."
For Stuttgart coach Armin Veh it was a second straight defeat since he replaced Giovanni Trapattoni last week.
Thursday's other tie produced a 2-1 home victory for Slavia Prague against Serie A side Palermo. Lukas Jarolim and Andrea Barzagli were on target for the Czechs, with Kewullay Conteh notching for Palermo.
All 16 second-leg ties take place next Thursday. The final is in Eindhoven on May 10.
