The first course aimed at training of military officers of the three Baltic States was introduced in 2004.

Since 2004 the international Air Force Captain Course was held at the General Jonas Zemaitis Military Academy of Lithuania.

In 2007 the Air Force Captain Course was renamed as the Air Force Junior Command and Staff Course.

By 2007 the total of 59 Air Force (AF) officers completed the latter course, mainly 17 officers of the Estonian AF, 20 of the Latvian AF, and 22 of the Lithuanian AF respectively.

 
While developing the concept of modern military training, the need to synchronise the military training of the Air Force Staff officers and those of the Land Force of the Baltic States has occurred; also, to ensure consistent Air Force officer training and better preparation for the Joint Command and General Staff Officer Course. Thus, the idea to organise the Air Force Intermediate Command and Staff Officer Course was born.

In 2007 the first Class of the Air Force Command and Staff Course began studies. 8 officers of the Lithuanian AF and 1 of the Latvian AF completed it.

In 2008 the Air Force Commanders of the three Baltic States decided to reorganise the Air Force Junior Command and Staff Course and Air Force Senior Command and Staff Course as the Air Force Command and Staff Course.

The Air Force Command and Staff Course is held once per year, beginning from August till end of December. This course comprises the total of 15 students, 5 per each Baltic State.
In the period 2004-2006 the Course was headed by Lt Col Audronis Navickas. At present Lt Col Eltonas Meleckis is the Course Director (AFCSC), apppointed in the middle of 2006.