It's not the boy's father who is missing but Dr. Wilmington, the previous owner of the house, but otherwise this is definitely "Same Time Next Year" (1993) by Neal Shusterman.
The girl, Marla Nixbok, does state that she should be living in a different time:
"I was born a hundred years too early," she often tells her friends. "I ought to be living in a future time where I wouldn't be surrounded by such dweebs."
The boy, Buford (Ford) Planct, is a new student who learns that Dr. Wilmingon disappeared and then tells Marla that Wilmington left a bunch of strange machines in his basement.
"Why? What's wrong with the place?" asks Ford, innocently.
"Nothing," says Marla, "except for the fact that it used to belong to old Dr. Wilmington, the creepiest professor Stanford University ever had."
Ford leans in to listen.
"One day," says Marla, "about seven years ago, Wilmington went into the house...and never came out."
Ford nods, not showing a bit of fear.
"Personally," says Marla, trying to get a rise out of him, "I think he was killed by an axe murderer or something, and he's buried in the basement."
But Ford only smiles. "I wouldn't be surprised," he says. "There's a lot of weird things down in our basement."
Marla is very interested, and manipulates Ford into taking her down into the basement, where she starts to uncover all the machines.
It takes Ford a while to figure them all out, but he discovers that they're all fundamentally flawed in some way, like the sonic shower that dissolves your skin.
Then, in a small root cellar off the basement they discover the time machine, or "Tempus Synchro-Epicyclus." They test it using a stuffed bear:
Together they run upstairs and find the perfect guinea pig; Ford's baby sister's teddy bear, Buffy. They bring Buffy down and set him on the silver chair.
They send Buffy three days into the future, but before they can verify that Buffy arrives safely, Marla gets in trouble with her parents and decides she must go to the future immediately.
Ford is worried that the machine isn't safe:
"Marla, the last person to touch that machine must have been Wilmington—and it was set for three days! If he went three days into the future, why didn't he come back?"
But Marla is determined and abuses Ford, finally scratching his face to get him to let her into the time machine. She sets it to go forward one year.
Ford finally figures it out, but Marla won't listen to him:
Ford crawls into the root cellar, out of breath.
"Marla, don't!" he screams.
"Get lost!" she shrieks back.
"But I figured it out!"
"Good. Does the machine work?"
"Yes, it does, but—"
"That's all I need to know!" Marla flips the switch and leaps into the silver chair. "See you next year!" she calls.
"Nooooooo!"
And she ends up in floating in space, far from Earth and the Sun.
But the Earth has long since moved on.
Even the sun is gone—just one among many distant stars.
Now she knows exactly why Wilmington and Buffy the bear can never come back. And as her last breath is sucked out of her lungs by the void of space, Marla Nixbok finally gets what she has always wanted: a crystal-clear vision of her own future. Now, and forever.
It has been collected in two collections of Shusterman's works, both titled Darkness Creeping, and in the Bruce Colville anthology Bruce Coville's Book of Spine Tinglers II: More Tales to Make You Shiver
