This is a compilation of district HQs in India, that do not have the same name as the district name, as of 2013. Particularly interesting ones are where there is a town by the district name, but the HQ is a different town. Many names in the list are based on river names, and a few regional references from older times. There are new ones, named after people. As the number of districts grow, perhaps this list will not be so large (as a proportion to the number of districts).
Much of this 'information' is gathered from wikipedia and a few government websites. Corrections and opinions welcome. This has not yet been updated to include Telangana, for example. Please send me an email if you wish to suggest any changes.
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West Bengal
District Headquarters that do not have the same name as the district name
Siuri - Birbhum
Tamluk - East Midnapur
Chinsura - Hooghly
Krishnanagar or Krishnagar - Nadia
Barasat - North 24 Parganas
Alipur - South 24 Parganas
Raiganj - North Dinajpur
Balurghat - South Dinajpur
Note: Dinajpur is in Bangladesh. Midnapur (Medinipur) is the now HQ of West Midnapur
District Headquarters that do not have the same name as the district name, although there is a town by that name!
English Bazar - Malda (although EB may be same as Malda)
Baharampur - Murshidabad
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Uttarakhand
District Headquarters that do not have the same name as the district name
Rudrapur - Udham Singh Nagar
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Uttar Pradesh
District Headquarters that do not have the same name as the district name
Robertsganj - Sonbhadra
Akbarpur - Ambedkar Nagar
Noida - Gautam Buddha Nagar - Noida
Gyanpyur - Sant Ravidas Nagar
Hathras - Mahamaya Nagar
Amroha - Jyotiba Phule Nagar
Akbarpur - Kanpur Dehat
Kasganj - Kanshi Ram Nagar
Manjhanpur - Kaushambi
Padarauna - Kushinagar
Lakhimpur or Kheri - Lakhimpur Kheri (borderline inclusion, because there are two distinct towns, it appears)
Khalilabad - Sant Kabir Nagar
Navgarh - Siddharth Nagar
Note: There are two Akbarpurs here in the list!
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Farukhabad - Fatehgarh
Orai - Jalaun
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Tripura
District Headquarters that do not have the same name as the district name
All four districts! Plus autonomous tribal area
Ambassa - Dhalai
Kailasahar - North Tripura
Udaipur - South Tripura
Agartala - West Tripura
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Tamil Nadu
District Headquarters that do not have the same name as the district name
Udhagamandalam - Nilgiris
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Nagercoil - Kanyakumari
For the time being, TN has gone back to older names. They may soon go back to naming districts after all the prominent people in the state, in which case this list will be a large one again. From the old days, an interesting one is Vellore - North Arcot and Cuddalore - South Arcot, and a somewhat obscure town called Arcot to the east of Vellore (and across the river from Wallajah - of Wallajah Road fame).
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Sikkim
District Headquarters that do not have the same name as the district name
All four districts
Gangtok - East Sikkim
Geyzing - West Sikkim
Mangan - North Sikkim
Namchi - South Sikkim
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Punjab
District Headquarters that do not have the same name as the district name
Nawanshahr - Shahid Bhagat Singh Nagar
Mohali - Sahibzada Ajit Singh Nagar (known naturally enough as SAS Nagar)
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Odisha
District Headquarters that do not have the same name as the district name
Chattrapur - Ganjam
Kandhamal - Phulbani
Paralekhamundi - Gajapati
Baripada - Mayurbhanj
Bhawanipatna - Kalahandi
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Bhubaneswar - Khordha
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Meghalaya
District Headquarters that do not have the same name as the district name
All seven districts!
Williamnagar - East Garo HIllis
Shillong - East Khasi Hills
Tura - West Garo Hills
Jowai - Jaintia Hills
Hongpo - Ri-bhoi
Baghmara - South Garo Hills
Nongstoin - West Khasi Hills
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Manipur
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Porompat - Imphal East
Lamphelpat - Imphal West
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Maharashtra
District Headquarters that do not have the same name as the district name
Alibag - Raigad
Oros - Sindhudurg (a new township called Sindhudurgnagari is taking shape)
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Lakshadweep
District Headquarters that do not have the same name as the district name
Kavaratti - Lakshadweep
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Kerala
District Headquarters that do not have the same name as the district name
Kalpeta - Wayanad
Painavu - Idukki
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Kakkanad - Ernakulam
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Karnataka
District Headquarters that do not have the same name as the district name
Madikeri - Kodagu
Mangalore - Dakshina Kannada
Karwar - Uttara Kannada
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Jharkhand
District Headquarters that do not have the same name as the district name
Jameshedpur - East Singhbhum
Chaibasa - West Singhbhum
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Himachal Pradesh
District Headquarters that do not have the same name as the district name
Reckong Peo - Kinnaur
Keylong - Lahaul and Spiti
Nahan - Sirmaur
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Dharamshala - Kangra
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Haryana
District Headquarters that do not have the same name as the district name
Nuh - Mewat
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Narnaul - Mahendragarh
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Gujarat
District Headquarters that do not have the same name as the district name
Godhra - Panchmahals
Ahwa - The Dangs
Himmatnagar - Sabarkantha
Palanpur - Banaskantha
Bhuj - Kachchh
Rajpipla - Narmada
Vyara - Tapi
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Goa
District Headquarters that do not have the same name as the district name
Panaji - North Goa
Margao - South Goa
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Dadra and Nagar Haveli
District Headquarters that do not have the same name as the district name
Silvassa - Dadra and Nagar Haveli
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Chhatisgarh
District Headquarters that do not have the same name as the district name
Jagdalpur - Bastar
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Bihar
District Headquarters that do not have the same name as the district name
Ara - Bhojpur
Motihari - East Champaran
Bettiah - West Champaran
Bhabua - Kaimur
Chhapra - Saran
Hajipur - Vaishali
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Sasaram - Rohtas (the winner in the list!)
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Assam
District Headquarters that do not have the same name as the district name
Silchar - Cachar
Mangaldai - Darrang
Guwahati - Kamrup
Diphu - Karbi Anglong
Haflong - North Cachar Hills
Tezpur - Sonitpur
Mushalpur - Baksa
Kajalgaon - Chirang
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Arunachal Pradesh
District Headquarters that do not have the same name as the district name
Hawai - Anjaw
Seppa - East Kameng
Pasighat - East Siang
Koloriang - Kurung Kumey
Tezu - Lohit
Roing - Lower Dibang Valley
Ziro - Lower Subansiri
Yupia - Papum Pare
Khonsa - Tirap
Anini - Upper Dibang Valley
Daporijo - Upper Subansiri
Ying Kinog - Upper Siang
Bomdila - West Kameng
Along - West Siang
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Andhra Pradesh
District Headquarters that do not have the same name as the district name
Eluru - West Godavari
Kakinada - East Godavari
Vijaywada - Krishna
Ongole - Prakasam
Hyderabad - Rangareddi
District Headquarters that do not have the same name as the district name, although there is a town by that name!
Sangareddi - Medak
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Andaman and Nicobar Islands
District Headquarters that do not have the same name as the district name
Mayabunder - North and Middle Andaman
Port Blair - South Andaman
Car Nicobar - Nicobar
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Rajasthan, Nagaland, Madhya Pradesh and Jammu and Kashmir - None