Sprint Corp. said it lost a net 336,000 contract subscribers in its September quarter, widening from the prior period, while it warned increased costs tied to customer upgrades will dent its profit for the year.

The wireless carrier lost 245,000 of the industry's most lucrative customers in the previous quarter and 535,000 a year earlier.

The company, which previously said it planned to cut an unspecified number of jobs, pegged that number at 2,000.

Pointing to increased costs tied to upgrade volumes in September when Apple Inc.'s latest iPhone went on sale and its significant loss of the most lucrative wireless contracts in recent quarters, Sprint estimated earnings before interest, taxes, depreciation and amortization of $5.8 billion to $5.9 billion for the year, down from $6.7 billion to $6.9 billion.

Shares fell about 3% after hours as the results missed expectations.

Meanwhile, the company has negotiated an amendment to its $3.3 billion bank credit facility, a person familiar with the matter said, after its financial performance threatened its compliance with key terms.

The facility, which was expanded in February, puts limits on how much debt Sprint can carry relative to its cash flow. The company is in the middle of a price war in the industry and faces expensive spectrum purchases in the years ahead.

Terms of the amendment couldn't immediately be learned. While the carrier is struggling to keep customers from leaving and emerge from years of losses, it benefits from the backing of deep-pocketed majority owner SoftBank Corp.

Sprint has been striving to turn itself around and in August appointed a new chief executive and abandoned its plans to acquire T-Mobile US Inc. The company's contract losses were initially due to the shutdown of its aging Nextel network and are more recently due in part to a massive network overhaul that has resulted in more dropped calls in areas where construction is taking place.

Sprint's total contract customer turnover rate was 2.18%, compared with 2.09% in the previous quarter and 1.99% a year earlier.

Overall for its second quarter Sept. 30, Sprint reported a loss of $765 million, or 19 cents a share, compared with a year-earlier loss of $699 million. Revenue increased to $8.49 billion.

Analysts polled by Thomson Reuters expected a per-share loss of six cents and revenue of $8.59 billion.

-Tess Stynes contributed to this article.

Write to Ryan Knutson at ryan.knutson @wsj.com

Access Investor Kit for SoftBank Corp.

Visit http://www.companyspotlight.com/partner?cp_code=A591&isin=JP3436100006

Subscribe to WSJ: http://online.wsj.com?mod=djnwires