Countries operating the Type 209 include Argentina, Brazil, Chile, Colombia, Ecuador, Greece, India, Indonesia, Peru, South Africa, South Korea, Turkey and Venezuela. All Type 209s remain in service except for ARA San Luis (S-32) which was stricken in 1997 after an incomplete overhaul and Glavkos S-110 decommissioned in 2011. Iran had an order for six Type-209 submarines that was cancelled by Khomeini in 1979.
The first user was the Hellenic Navy which purchased four Type 209/1100 and four Type 209/1200 submarines.
The largest operator of the Type 209 is the Turkish Navy which operates six Type 209/1200 submarines (commissioned between 1976 and 1989) and eight Type 209/1400 submarines (commissioned between 1994 and 2007). At present, the Turkish Navy is also the largest operator of German designed submarines in the world.
Three new Type 209/1400 submarines were delivered to South Africa in 2006, costing $285 million each.
Type 209s are often supplemented with other submarine designs or are scheduled to be replaced by them. Argentina received two TR-1700 class submarines (Santa Cruz class) during the 1980s. Ten Kilo class submarines were purchased by India in the 1980s and 90s (Sindhughosh class submarine), along with Akula class submarine INS Chakra in 2011. Two Scorpène class submarines have been commissioned by Chile, while Brazil has four and India has six ships ordered or under construction. Nine Type 214 submarines (Son Won-il class) are commissioned, building, or planned by South Korea to supplement its force, while Greece is replacing its aging Glaukos class with four Type 214 submarines (Papanikolis class), and Turkey will be replacing early Atilay class ships with six Type 214 submarines.
During the Falklands War the Argentinian Type 209/1200 submarine "San Luis" performed a war patrol. While on their way to the area assigned the fire control computer went out of order. The vessel continued on to the combat area, and managed to fire at least 3 wire guided SST4 mod0 torpedoes at the British fleet. The torpedoes suffered from various issues, with the guide wire cut a minute after launch and the torpedoes going off the assigned course. After the war testing revealed that the torpedoes electric gyroscopes had reversed polarity, which resulted in a complete refit of the entire Argentinean torpedo stock, and a conversion of a portion of this stock from Mod0 to Mod1, performed by the firm which produced these weapons (AEG). Beside the torpedo issue, "San Luis" patrolled mostly undetected.
On 31 August 2012, the Egyptian Navy commander General Osama Ahmed stated that a contract has been signed with the German side to build two type 209 submarines for the Egyptian Navy including the latest technology this type has reached. The first vessel is scheduled to be delivered in 2016. Egypt is planning to exercise an option of the contract for another two type 209 submarines.