Portsmouth owner Vladimir Antonov has been arrested following an inquiry into asset stripping.
An arrest warrant was issued for the 36-year-old and his business partner Raimondas Baranauskas on Wednesday.
Lithuanian prosecutors want to question the pair over alleged money laundering and fraud involving Snoras Bank. Both men deny any wrongdoing.
Antonov owns 68% of the bank, which went into temporary administration last week.
"In response to a Europe-wide arrest warrant officers arrested a 36-year-old man in London this afternoon," said City of London Police.
Another of Antonov's banks, Krajbanka, had their operations suspended last week.
