Pyelonephritis: This is the most likely diagnosis due to the combination of fever and flank pain, which are classic symptoms of an upper urinary tract infection. Pyelonephritis involves infection of the kidney and can cause significant morbidity if not treated promptly.

Nephrolithiasis (Kidney Stones): While kidney stones can cause severe pain, the presence of fever suggests an infectious component, which might not be the primary issue in nephrolithiasis. However, stones can obstruct the urinary tract and lead to infection.
Urinary Tract Infection (UTI) with Obstruction: Similar to pyelonephritis, a UTI with an obstructing stone or other cause can lead to fever and flank pain due to the infection and possible pyelonephritis.
Perinephric Abscess: An abscess around the kidney can cause fever and flank pain, often as a complication of pyelonephritis.

Sepsis due to any Cause: Sepsis is a life-threatening condition that can arise from any infection, including those causing fever and flank pain. Early recognition and treatment are crucial.
Emphysematous Pyelonephritis: A severe, necrotizing infection of the kidney, more common in diabetic patients, which can rapidly progress to sepsis and death if not promptly treated.
Pneumonia: While pneumonia primarily causes respiratory symptoms, it can occasionally refer pain to the flank area, especially if the infection involves the lower lobes of the lungs.

Renal Infarction: A blockage of the renal arteries can cause severe flank pain and possibly fever, though it's less common than infectious causes.
Renal Cell Carcinoma with Infection: A tumor of the kidney can become infected, leading to fever and flank pain, though this would be an unusual presentation for cancer.
Tuberculosis of the Kidney: Genitourinary tuberculosis can cause chronic symptoms including flank pain and fever, though it's relatively rare in many parts of the world.