Change your furnace filter with a high allergen reducing one, close the windows, turn the fan from "auto" to "on", then vacuum the entire house including cloth furniture every day for a week, and launder all the large cloth items (blankets, sheets, rugs) once. This will reduce the possible allergens in the house significantly, and you should see improvement if that's the issue. If it is, you only have to vacuum/launder once a week after the initial get-rid-of-all-dust session, and replace your furnace filter once a month if you choose to use it rather than a dedicate HEPA filter in the area she spends most time in.
Also note that it's allergy season, so if she's young and this is a new issue, even though she's indoor the outside pollen can affect her if you leave the windows open. Consider shutting the house up and seeing if that results in improvement.
If it is allergens, then you need to figure out if its outside or inside once she's feeling better. Taking her on walks outside should quickly determine if it's an outside thing, and if so it's going to be seasonal and antihistamines might be your best bet.
If its inside, then vacuuming and filtering should be sufficient.
