The Muslim Empires founded by people of Indus Valley/Modern Pakistan over the Ganges plains/Modern India.

1) Lodhi dynasty–a Pashtun dynasty that ruled the Delhi Sultanate from 1451 to 1526. It was founded by Bahlul Lodhi in 1451 after the abdication of last Sayyid Sultan.
Bahlul was born in Multan in Lodhi tribe and was grandson of Malik Bahram Khan. According to Ain-i-Akbari Bahram Khan moved from Dera Ismail Khan (KPK) to Multan in search of good opportunities and later took service under the governor of Multan.

(Coins issued by Bahlul Lodhi)
Lodhis are famous to revive somehow the lost glory of Delhi Sultanate, surpress the rebellions in Punjab and Gangetic plains, transfer the capital from Delhi to newly established city of Agra and conquering many kingdoms including the powerful Sultanate of Jaunpur.
2) Sayyid dynasty– a Punjabi dynasty that ruled the Delhi Sultanate from 1414 to 1451. It was founded by Khizr Khan belonging to Khokar clan after the death of last Tughluq monarch. He succeeded to capture Delhi by taking advantage of chaos created because of Timurid invasion.
The founder of dynasty didn't adopt the title of Sultan because of respect of Imperial house of Timur, instead he adopted the titles of "Rayat-i-Ala" (Sublime Banners) and "Masnad-i-Aali" (Most High Post). But yes his successors adopted the titles of Shah & Sultan-e-Azem.
Sayyid Sultans succeeded to surpress somehow the rebellions of Rajputs, Gwailor, Punjab and Katehar.

It is important to note that dynasty adopted the noble title of Sayyid because of title's social stature and most probably it had nothing to do with Arab ancestry.
3) Khokhar Confederacy– a Punjabi confederacy led by Khokhar cheifs succeeded to capture Delhi for short period of time during the reign of Sultan Mubarak Shah of Sayyid dynasty.
Khokhars under the Jasrath conquered many significant areas of Indus plains including Punjab, KPK, Jammu, Haryana, Himachal Pardesh and ultimately moved towards Ganges plains and conquered Delhi in 1431 but later on September of 1432, they were driven out of Delhi by Sayyids.
References

C.E. Bosworth, The New Islamic Dynasties, (Columbia University Press, 1996)

Ain-i-Akbari, translated into English by H.S.Jarret

Mahajan, V.D. (1991, reprint 2007). History of Medieval India, New Delhi: S. Chand
India in the Persianate Age: 1000-1765 by Richard M. Eaton

After Timur Left: Culture and Circulation in Fifteenth-Century North India

Nelson, Wright [1974], The Coinage & Metrology of the Sultans of Dehli

Multan District. Punjab (India): Civil and Military Gazette Press. 1902.
Elliot, Henry Miers; Dowson, John (1872). The History of India, as Told by Its Own Historians: The Muhammadan Period

Gaṇeśadāsa, Baḍehra (1991). Billawaria, Anita K (ed.). Rājdarshani: a Persian history of north-western India from earliest times to A.D. 1847.
Once again I want to clarify that I am not calling these empires as Pakistani empires but the empires which were founded by the ancestors of modern day Pakistanis or by the people of Indus.

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