The Lithuanian decision, which includes deliveries of steel, coal and building materials to the Russian enclave, will take effect on Saturday.
According to the country's authorities, they only follow the EU's sanction rules against Russia.
According to Gabrielius Landsbergis, Lithuania's Foreign Minister, the decision has been reconciled with the European Commission.
Kaliningrad is sandwiched between Poland and Lithuania on the Baltic Sea and is therefore dependent on imports.
According to the region's Russian governor Anton Alikhanov, Lithuania's decision affects up to 50 percent of all goods that the Russian enclave currently imports via Lithuania, writes Reuters.
He also says that it is possible to get around the problem with the help of transport from the sea.
Russia promises countermeasures
The Russian government has reacted strongly to the decision, which they call both illegal and openly hostile.
- The situation is beyond serious.
The decision has no equivalent.
It is a crime against everything, says Kremlin spokesman Dmitry Peskov at a press conference.
Russia's Foreign Ministry has summoned both Lithuania's top envoy and EU ambassador.
"If the transport of goods between Kaliningrad and the rest of the Russian Federation via Lithuania is not completely restored in the near future, Russia will take the right to take measures to defend its national interests."
writes the Foreign Ministry in a statement, according to Reuters.