The first Count Rapoto I of Ortenburg was mentioned about 1134. Born at Kraiburg, the fourth son of Duke Engelbert II of Carinthia, he retained several Bavarian territories held by the Spanheimer family, while his elder brothers Ulric and Engelbert III succeeded their father in Carinthia and Istria. Rapoto had the Ortenburg Castle erected about 1120 whereafter he began to call himself a Graf von Ortenberg. When his brother Engelbert III died without heirs in 1173 he could unite a significant number of territories under his rule and confirmed his independence when the Bavarian ducal title passed to the House of Wittelsbach in 1180. After Otto VIII of Wittelsbach had assassinated the German king Philip of Swabia in 1208, Rapoto's son Count Rapoto II even held the office of a Count Palatine of Bavaria.

Rapoto's II descendants however soon entered into fierce conflicts with the neighbouring Bishops of Passau and also with the mighty Austrian House of Babenberg. Upon the death of Count Rapoto III in 1248, his territories as well as the office of the Count Palatine again passed to the Wittelsbachs. The Ortenburg territory was further diminished by an ongoing inheritance conflict between Rapoto's III nephew Henry II and his brothers, of which the surviving Count Rapoto IV in 1275 could only retain the lands around Ortenburg Castle. Upon the death of Count Henry IV of Ortenburg in 1395, the county was partitioned into Ortenburg-Neuortenburg and Ortenburg-Dorfbach. The Neuortenburg branch again inherited the Dorfbach county in 1462 following the death of Count Alram II. Meanwhile the county had fallen under the influence of the Wittelsbach Bavaria-Landshut duchy, and also sided with Duke Albert IV of Bavaria-Munich in the 1503 Landshut War of Succession. Since the dynasty of the Counts of Celje had become extinct with the death of Count Ulrich II in 1456, the Ortenburg counts had claimed the Carinthian Grafschaft Ortenburg, but failed to prove any kinship apart from the name similarity.

Under Count Joachim of Ortenburg-Neuortenburg, the state turned to Protestantism in 1563, fiercely opposed by Duke Albert V of Bavaria challenging Ortenburg's Imperial immediacy which however was confirmed by the Imperial Chamber Court in 1573. The county remained a Lutheran enclave within the mainly Catholic Bavarian lands and became a refuge for expellees during the Thirty Years' War. Though deeply in debt after numerous processes against the Wittelsbach dukes, Ortenburg-Neuortenburg retained its independence until in 1805 Count Joseph Charles Leopold finally sold it to Elector Maximilian I Joseph of Bavaria. The county was incorporated into the newly established Kingdom of Bavaria in the course of the Empire's dissolution in 1806. 

Counts of Ortenburg

* Rapoto I (1134 - 1186), also Count of Murach from 1163 and Count of Kraiburg from 1173 on
* Rapoto II (1186 - 1231), son, Count of Kraiburg and Count Palatine of Bavaria from 1209 on, jointly with his brother
o Henry I (1186 - 1241), also Count of Murach 1186 - 1238
* Rapoto III (1231 - 1248), son of Rapoto II, Count of Kraiburg, also Count Palatine of Bavaria, died without male heirs
* Henry II (1241 - 1257), son of Henry I
o Gebhard (1238 - 1272), brother, Count of Murach 1238 - 1272, Imperial Count of Ortenburg 1257 - 1275, and
o Rapoto IV, brother, Count of Murach 1238 - 1272, Imperial Count of Ortenburg 1275 - 1296
* Henry III (1297/1321 - 1345), son of Rapoto IV
* Henry IV, son of Henry III (1346 - 1395)

Counts of Ortenburg-Neuortenburg - 1395 - 1806

* George I (1395 - 1422), son of Henry IV
* Henry V (1422 - 1451)
* Sebastian I (1451 - 1495)
* Ulrich II (1495 - 1524)
* Sebastian II (1524 - 1559)
* Joachim (1559 - 1600)
* Henry X (1600 - 1603)
* Frederick Casimir (1603 - 1658)
* George Reinhard (1658 - 1664)
* Christian (1664 - 1684)
* George Philip (1684 - 1702)
* John George (1702 - 1725)
* Charles III (1725 - 1776)
* Charles Albert (1776 - 1787)
* Joseph Charles Leopold (1787 - 1806)