The Bogdanci area has been settled since the antiquity. The oldest settlement is 1 km north-west called Gorno selo, with a remains of rocks, building materials & shingle. Several vessels have been found 1,5-2 km south of Bogdanci in the Pobreško district, while remains of a wall exist 3-4 km north-west in the Mamino district.
According the a legend, Bogdanci was by the first settler Bogdan, who settled near the gorges that he used for his cattle. Although there is not older data, there is some information from the 17th-18th century, which occurs in connection with some Turkish blood taxes. According to them, Bogdanci is a settlement.
Meanwhile, we have a written document titled "Description of Bogdanci", that originates from May 30th 1891, that describes Bogdanci as a settlement located north-east from Gevgelija (8 km). According to the document, Bogdanci has a church and 600 houses with 3,500 inhabitants who amuse with agriculture.
There are several other documents with different historical timeline, that provide information on Bogdanci. According one linguistic statistics from 1880, the town (then a village) had 3,560 inhabitants - 2,540 Macedonians, 900 Turks and 120 Roma. A document from 1905 says that there are 3,184 inhabitants - without Turks listed in it.
Several armed gangs lead by the dukes, were operating in surroundings of Bogdanci before the Ilinden rebellion. Their mission was to disable as much Ottoman Turks & traitors as possible, and to prepare the locals for the incoming rebellion. A report of a Serbian consul from Salonica mentions that 27 people from Bogdanci, have joined these gangs.
During the rebellion in August 1903 around 80 people from Bogdanci headed towards the gangs. On August 24th 1903 they have disabled the railway and killed many Turkish soldiers at a battle. These gangs were active until September, when the local leader, Adzi Mito helped them to retreat, inviting the Ottomans at feast in Bogdanci.
The Bogdanci area wasn't spared at the period of the Balkan Wars (1912-1913). The Serbian army, followed by the Greek and later Bulgarian, have entered Bogdanci after the end of the First Balkan War in 1912.
The Serbs have established their authority in Bogdanci after 1913, that resulted with a Serbian language in schools and church.
During the First World War, being almost on the frontline and occupied by the German and Bulgarian troops, Bogdanci was turned into a military base. The citizens of Bogdanci were forced to work for the army on the Macedonian Front (1916-1918). Very soon, along with the citizens of Dojran and Gevgelija were evacuated on the north, in Valandovo, Strumica and some even in Kumanovo or Niš (Serbia).
When Yugoslavia was attacked and occupied by the Axis forces during the Second World War, the citizens of Bogdanci have actively taken part in the war for national liberation.
After the liberation of Macedonia in 1945, Bogdanci along with all enclosed difficulty and weaknesses has started to develop in all the areas, and especially in the area of agricultural production. Very soon the life standard of its inhabitants has developed.