The 24-year-old was last seen at Lake Como and is understood to have been involved in a swimming accident before she went missing.
Ismaili played for Switzerland in the Algarve Cup earlier this year and is a regular first choice for head coach Nils Nielsen.
A statement on Young Boys' official website said: "The officials of the BSC Young Boys have been informed that our player Florijana Ismaili has been missing since Saturday afternoon on Lake Como after a swimming accident.
"Searches by the police continue. We are very concerned and have not given up the hope that everything will turn out well.
"We are in close contact with family members and we ask for your understanding that we cannot provide any further information at the present time.
"We will inform again as soon as we know more."
Police searched the lake on Saturday evening, before calling the search off. The mission was resumed early on Sunday morning, but as yet has yielded no results.
“We’ve been up since 8 o’clock this morning,” rescue director Giuseppe Camassa told Swiss newspaper Blick .
“We take a rubber dinghy around the area [where Ismaili was last seen] in a two kilometre radius. So far in vain.
“Helicopters and divers will arrive later in the day. Lake Como is treacherous. It has strong currents under the calm waters.”
The helicopter and dive teams are busy at another emergency in Milan.
The Italian authorities have spoken to the paper, admitting they did not know the circumstances surrounding the player’s disappearance.
“We do not know yet exactly what happened,” a police spokesperson said.
“It could be that the young woman fainted when she jumped into the cold water.”
Ismaili is the club captain at Young Boys. She scored seven goals last season, which made her the team’s top scorer.
She has made 33 appearances for the Switzerland national team, including an appearance just a fortnight ago.
She was in the squad for the 2015 World Cup but did not make it off the bench at the tournament.