Direct flights from Copenhagen to Estonia:

Copenhagen to Tallinn

Flights from Copenhagen to Estonia with 1 stopover:

Flights via Oslo Gardermoen (OSL), Norway
From Copenhagen (CPH), Denmark with Norwegian
OR
From Copenhagen (CPH), Denmark with Estonian Air
OR
From Copenhagen (CPH), Denmark with SAS
Transfer at Oslo Gardermoen (OSL), Norway Then on to Tallinn (TLL), Estonia with Norwegian
OR
Then on to Tallinn (TLL), Estonia with Estonian Air
OR
Then on to Tallinn (TLL), Estonia with SAS
Flights via Helsinki Vantaa (HEL), Finland
From Copenhagen (CPH), Denmark with Finnair Transfer  at Helsinki Vantaa (HEL), Finland Then on to Tallinn (TLL), Estonia with Finnair
OR
Then on to Tartu (TAY), Estonia with Finnair
Flights via Stockholm Arlanda (ARN), Sweden
From Copenhagen (CPH), Denmark with Estonian Air
OR
From Copenhagen (CPH), Denmark with SAS
Transfer at Stockholm Arlanda (ARN), Sweden Then on to Tallinn (TLL), Estonia with Estonian Air
OR
Then on to Tallinn (TLL), Estonia with SAS
Flights via Riga International (RIX), Latvia
From Copenhagen (CPH), Denmark with airBaltic Transfer at Riga International (RIX), Latvia Then on to Tallinn (TLL), Estonia with airBaltic
Flights via Warsaw (WAW), Poland
From Copenhagen (CPH), Denmark with LOT Transfer at Warsaw (WAW), Poland Then on to Tallinn (TLL), Estonia with LOT
Flights via Stockholm Bromma (BMA), Sweden
From Copenhagen (CPH), Denmark with Flybe
OR
From Copenhagen (CPH), Denmark with Finnair
Transfer at Stockholm Bromma (BMA), Sweden Then on to Tallinn (TLL), Estonia with Flybe
OR
Then on to Tallinn (TLL), Estonia with Finnair
Flights via Moscow Sheremetyevo (SVO), Russia
From Copenhagen (CPH), Denmark with Aeroflot Transfer at Moscow Sheremetyevo (SVO), Russia Then on to Tallinn (TLL), Estonia with Aeroflot
Flights via Brussels International (BRU), Belgium
From Copenhagen (CPH), Denmark with Brussels Airlines Transfer at Brussels International (BRU), Belgium Then on to Tallinn (TLL), Estonia with Brussels Airlines
Flights via Munich (MUC), Germany
From Copenhagen (CPH), Denmark with Lufthansa Transfer at Munich (MUC), Germany Then on to Tallinn (TLL), Estonia with Lufthansa
Flights via St Petersburg Pulkovo (LED), Russia
From Copenhagen (CPH), Denmark with Rossiya Airlines Transfer at St Petersburg Pulkovo (LED), Russia Then on to Tallinn (TLL), Estonia with Rossiya Airlines
Flights via Amsterdam (AMS), Netherlands
From Copenhagen (CPH), Denmark with KLM Transfer at Amsterdam (AMS), Netherlands Then on to Tallinn (TLL), Estonia with KLM
Flights via Prague (PRG), Czech Republic
From Copenhagen (CPH), Denmark with Czech Airlines Transfer at Prague (PRG), Czech Republic Then on to Tallinn (TLL), Estonia with Czech Airlines
Flights via Frankfurt am Main (FRA), Germany
From Copenhagen (CPH), Denmark with Lufthansa Transfer at Frankfurt am Main (FRA), Germany Then on to Tallinn (TLL), Estonia with Lufthansa
Flights via Paris Charles de Gaulle (CDG), France
From Copenhagen (CPH), Denmark with Air France Transfer at Paris Charles de Gaulle (CDG), France Then on to Tallinn (TLL), Estonia with Air France
Flights via Kiev Borispol (KBP), Ukraine
From Copenhagen (CPH), Denmark with Aerosvit Airlines Transfer at Kiev Borispol (KBP), Ukraine Then on to Tallinn (TLL), Estonia with Aerosvit Airlines
Flights via Trondheim (TRD), Norway
From Copenhagen (CPH), Denmark with SAS Transfer at Trondheim (TRD), Norway Then on to Tallinn (TLL), Estonia with SAS
Flights via Tallinn (TLL), Estonia
From Copenhagen (CPH), Denmark with Estonian Air Transfer at Tallinn (TLL), Estonia Then on to Tartu (TAY), Estonia with Estonian Air