In 2012–13, the club participated in the 2012–13 UEFA Europa League, reaching the Round of 16 before being eliminated by Fenerbahçe. They finished the season by winning the Czech league for the second time.
In 1911 Jaroslav Ausobský, an official of the state railways, filed a request for the establishment of a new football club in Plzeň. In August of that year the newly formed team Viktoria played their first match, losing 7-3 against Olympia Plzeň.
For the first eighteen years of its existence, Viktoria Plzeň was a purely amateur club, although in 1922–1923 they took their first foreign trip to Spain, where they won six out of nine games. In June 1929 an extraordinary meeting of members agreed to go professional and enter the national professional league. Viktoria finished their first season in seventh place, but the very next season, improved and reached second place, which meant a first-ever promotion to the premier league. In the 1934–35 Czechoslovak First League, Viktoria finished in fourth place and subsequently played in the 1935 Mitropa Cup, the top European club competition at the time. Two matches against Juventus of Italy brought Viktoria to the attention of European football at large. They drew 3-3 at home, but lost 5-1 in Italy.
Viktoria played with success in the premier league, being relegated back down to divisions for the 1938 season but returning to top competition the next year. The outbreak of World War II interrupted competition, notably through the absence of teams from Slovakia. In 1942 Viktoria fell again into the divisions, but again returned to the top league the next year, where they would remain until 1952. That same year the club changed its name to Sokol Škoda Plzeň. For nine years they remained in the divisions, struggling to return to the premier league, and in 1961, now under the name of Spartak Plzeň, achieved that promotion. The club was relegated and promoted frequently between the top two tiers until 1972, when as Škoda Plzeň they settled in the premier league for eight years.
In 1971, Viktoria won the Czech Cup by drawing lots after the two-legged final ended 4-4 on aggregate and 5-5 in a limited penalty shootout against Sparta Prague B. They lost 7-2 on aggregate in the Czechoslovak Cup final against Slovak Cup winners Spartak Trnava, but as Trnava had won the league title that season, Viktoria was the country's entrant to the next season's Cup Winners' Cup. The club was eliminated in the first round by Bayern Munich of West Germany, 7-2 on aggregate. From 1980 until the division of Czechoslovakia 13 years later, Viktoria moved frequently between the top two tiers again.
Pavel Horváth was voted as Viktoria's best player of all time at the club's centenary gala in 2012.
In 1992, the club returned to its historical name FC Viktoria Plzeň and the very next season, advanced to the first league, where it remained until 1999.
In the first years of the new millennium, Viktoria was owned by a foreign investor - Italian Football Company Ltd EAST. This situation lasted until March 2005, when 100% of the club's shares were bought by local interests. The Summer of 2005 also brought back relations with the Czech motor company Skoda, who had previously been the club's name sponsors.
The club's Stadion města Plzně was also rebuilt in 2011. On 11 June 2011 Viktoria celebrated together with fans in the courtyard of the Pilsner Urquell brewery for a centennial anniversary. In January 2012, the club held a festive gala for its centenary, and voted current midfielder Pavel Horváth as its greatest player of all time.
The 2011–12 season saw Viktoria finish in third place in the league, three points behind champions Slovan Liberec, to qualify for a third consecutive Europa League campaign. Starting in the second qualifying round, the club advanced past Metalurgi Rustavi of Georgia and Ruch Chorzów of Poland to set up a play-off against the Belgian club Lokeren, in which Viktoria advanced on away goals after a 2-2 aggregate draw. The club finished first in Group B, above the tournament's reigning champions, Atlético Madrid. In the round of 32, Viktoria were drawn against Napoli of Italy, and won 3-0 away and 2-0 at home to advance to the last 16, where they played Fenerbahçe of Turkey. Viktoria lost the home leg 1-0, and in the away leg (which was played behind closed doors due to the Istanbul club's fans' recent conduct) drew 1-1, nevertheless being eliminated from the competition. Viktoria won the Czech league for a second time at the end of the 2012-13 season.
The following is a list of the all-time statistics from Plzeň's games in the three UEFA tournaments it has participated in, as well as the overall total. The list contains the tournament, the number of seasons (S), games played (P), won (W), drawn (D) and lost (L). The statistics include qualification matches.