In April 2007, Stanimir Stoilov was assigned as caretaker manager of the Bulgaria national team for the matches against Belarus in June from the Euro 2008 qualification campaign.

He led them to winning the Bulgarian cup in 2009, but quit after the club failed to reach the group stage of the Europa League.

During the summer and autumn of 2009 Bulgaria won against Latvia 1–0 in a friendly and against Montenegro with 4–1, but then Stoilov suffered his first loss with the national team against Italy with 2–0.

The draw for UEFA Euro 2012 resulted in Bulgaria finding itself in a qualifying group with England, Switzerland, Wales and Montenegro.

Astana was entitled to play in the second qualifying round of the 2015–16 UEFA Champions League, where Stoilov's team eliminated NK Maribor.

He was appointed as a manager in one of the worst moments in the club's history, ranking 10th in the league standings after the first 6 games with 4 losses and just 2 wins and in a very bad financial state.

A few days after his appointment he released three players – Simeon Slavchev, Valeri Bojinov and Hristofor Hubchev and signed two younger – José Córdoba from Etar and Dimitar Kostadinov from Septemvri Sofia.

In the upcoming transfer window, Stoilov released 6 players – Gjoko Zajkov, Christos Shelis, Ivaylo Naydenov, Borislav Tsonev, Georgi Aleksandrov and Martin Petkov, and signed just as many – defenders Kellian van der Kaap and Noah Sonko Sundberg, Bulgarians Iliyan Stefanov from Beroe and Filip Krastev (on loan from Belgian Lommel), both attacking midfielders.

In the second half of the season the team showed tremendous improvement winning 11 league games, drawing 2 and losing 2 finishing 4th in the final standings.

In the quarter-finals, the team eliminated Septemvri Sofia with a 2–0 home win, and then faced Ludogorets in the semis, knocking them out with 4–2 aggregate score.

Throughout the whole tournament, Stoilov gave chance to the reserve goalkeeper of Levski – born in 2004 – Plamen Andreev, who started in each of the six matches, conceding only 2 goals (both in the first leg game against Ludogorets).