On 1 April 2006, Tom won their third match in a row at the start of the season and became the sole leaders of the Russian Premier Liga. This was only their second year in the top flight

In their debut season, Tom beat Zenit St. Petersburg at home, took points away from CSKA Moscow and Lokomotiv Moscow, and finished in 10th place. Then the team's top scorer Aleksey Medvedev (with five goals) moved to Krylia Sovetov Samara, and a 22-year-old Pavel Pogrebnyak was purchased as a replacement by Spartak.

The head coach also changed. In place of Anatoly Byshovets, Tom were managed by Valeriy Petrakov, who had already worked at the club from 2001 to 2003.

Tom had to play the opening match of the 2006 season in Moscow against Torpedo. The visitors scored the first goal of the championship through Alexander Kulchiy and won 2-1 thanks to an own goal by George Jokic in the 88th minute.

On the second matchday, Tom hosted Yuriy Semin’s Dynamo Moscow - featuring Sergey Ovchinnikov, Dmitry Khokhlov, Aleksey Smertin, Igor Semshov and Danny - but again won thanks to a goal from Branislav Krunic. Incidentally, the Serb had also scored in the same fixture the year before as Tom fought back from 2-0 down to win 3-2.

On 1 April, Tom met Shinnik Yaroslavl on the road. Shinnik had drawn 1-1 against Dynamo Moscow in their first home game of the season before being thrashed 5-1 by CSKA Moscow. Tom failed to take two glorious chances in the first half; both Krunic's penalty and Pogrebnyak's shot were blocked by home goalkeeper Evgeniy Safonov.

They had to wait until the 75th minute for Bulgarian Alexander Mladenov to catch the goalkeeper out, scoring the winning goal from a free kick.

By that time, the Moscow Derby at the Luzhniki had already ended. CSKA, who had also started the championship with two consecutive wins, drew with Spartak. The Armymen led 1-0 after a goal by Vagner Love, but were soon reduced to 10 men when Igor Akinfeev was sent off for handling the ball outside the penalty area.

Vladimir Gabulov came on to make his debut for CSKA, and immediately conceded from a close-range Yegor Titov shot. The draw in Moscow, along with their victory in Yaroslavl, put Tom in first place in the RPL. "This is no time for April Fools' jokes. Everything is serious," concluded the Football of Russia match report on Sport TV channel.

"We don't expect much," Petrakov admitted in an interview with Sport-Express newspaper after the match. “Let them write less about us. It is still difficult for us to chase the capital's great sides in this regard.

“The main game of the matchday took place in Moscow. And I don't attach much importance to the fact that Tom became the sole leaders. After all, only three matchdays have been played. If only there were three matchdays left…”

FC Tom were the league leaders for a week. On 8 April, they again played at the Luzhniki, this time against CSKA. They simply couldn’t contain Jo, who hit a double, and Gabulov failed to score in a 2-0 defeat. Valery Gazzaev’s team thus displaced their opponents from the top of the table and finished the championship there. Tom also fulfilled the task set by the management by finishing eighth - the best finish in their RPL history.